{"gene":"TBC1D15","run_date":"2026-04-28T21:42:58","timeline":{"discoveries":[{"year":2012,"finding":"Fis1 acts as a mitochondrial receptor that directly recruits TBC1D15 to the mitochondrial outer membrane; bacterially expressed Fis1 and TBC1D15 form a direct and stable complex, and TBC1D15 (normally cytoplasmic) relocalizes to mitochondria when co-expressed with Fis1. Knockdown of TBC1D15 induces highly developed mitochondrial network structures, placing TBC1D15 in regulation of mitochondrial morphology independently of Drp1.","method":"Co-immunoprecipitation from HeLa cell extracts, bacterial reconstitution of direct complex, fluorescence microscopy of co-expressed proteins, siRNA knockdown with morphological readout","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1–2 — direct binding reconstituted in vitro plus reciprocal co-IP plus localization experiment with functional consequence; replicated concept across multiple methods in same study","pmids":["23077178"],"is_preprint":false},{"year":2010,"finding":"TBC1D15 functions as a Rab7 GTPase-activating protein (GAP) in cells, reducing Rab7 binding to its effector RILP (measured by effector pull-down assay), fragmenting lysosomes, and conferring resistance to growth factor withdrawal-induced cell death. TBC1D15 GAP activity is selective for Rab7 and does not affect Rab4-, Rab5-, or Rab11-dependent processes.","method":"Effector pull-down assay (RILP-Rab7-GTP binding), lysosomal morphology imaging, cell death assays, transferrin recycling assay as selectivity control","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — cell-based GAP activity assay with multiple orthogonal readouts (effector binding, organelle morphology, cell survival, selectivity controls); highly cited foundational study","pmids":["20363736"],"is_preprint":false},{"year":2017,"finding":"Crystal structures of the TBC1D15 GAP domain (shark and pig orthologs) were solved to 2.8 Å and 2.5 Å resolution, revealing conservation with but distinct variations from yeast Gyp1p and TBC1D1. Active-site mutagenesis (Arg→Ala or Lys) of the catalytic arginine and glutamine residues abolishes GAP activity, confirming the dual-finger catalytic mechanism.","method":"X-ray crystallography, in vitro GAP activity assay, active-site mutagenesis","journal":"Protein science","confidence":"High","confidence_rationale":"Tier 1 — crystal structure combined with mutagenesis and in vitro enzymatic assay","pmids":["28168758"],"is_preprint":false},{"year":2013,"finding":"TBC1D15 is identified as a Numb-associated protein by large-scale affinity purification/mass spectrometry; its amino-terminal domain disengages p53 from the Numb–p53 complex, triggering p53 proteolysis and promoting stem cell self-renewal. TBC1D15 protein levels are reduced by autophagy-mediated degradation upon nutrient deprivation.","method":"Affinity purification and tandem mass spectrometry, co-immunoprecipitation, domain-mapping with deletion constructs, p53 stability assays, autophagy inhibitor experiments","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2–3 — MS-identified interaction confirmed by co-IP with domain mapping and functional readout, single lab","pmids":["23468968"],"is_preprint":false},{"year":2013,"finding":"Depletion of TBC1D15 in HeLa cells induces RhoA activation and membrane blebbing, which is abolished by RhoA signaling inhibitors. TBC1D15 is also required for proper accumulation of RhoA at the equatorial cortex during cytokinesis, establishing a role for TBC1D15 in RhoA-mediated cortical dynamics.","method":"siRNA knockdown, RhoA activity assay (pull-down), pharmacological inhibition of RhoA, fluorescence microscopy of cytokinesis","journal":"Molecular and cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 — KD with defined phenotypic readout and pathway placement via pharmacological rescue, single lab","pmids":["24337944"],"is_preprint":false},{"year":2019,"finding":"Annexin A6 promotes Rab7 inactivation by stimulating TBC1D15 (Rab7-GAP) activity; AnxA6 depletion in NPC1 mutant cells leads to Rab7 activation, peripheral redistribution of late endosomes, and enhanced cholesterol export to lipid droplets via StARD3-dependent membrane contact sites between late endosomes and ER.","method":"Co-immunoprecipitation, effector pull-down (Rab7-GTP), fluorescence live-cell imaging, electron microscopy of membrane contact sites, ACAT inhibitor assays","journal":"Cellular and molecular life sciences","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods placing TBC1D15 in an AnxA6–Rab7 axis, single lab","pmids":["31664461"],"is_preprint":false},{"year":2020,"finding":"TBC1D15 regulates mitochondria-lysosome contacts through both its Fis1-binding domain and its Rab7 GAP domain; overexpression loosens abnormal mitochondria-lysosome contacts, restores lysosomal size and function, and rescues mitophagy flux after myocardial infarction. Interference with either domain individually abrogates the beneficial effects.","method":"Transmission electron microscopy, live-cell time-lapse imaging, adenoviral overexpression, domain-mutation rescue experiments, mitophagy flux assays (fluorescence and western blotting), cardiac functional assessment","journal":"Theranostics","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods with domain-specific mutant controls, in vitro and in vivo validation","pmids":["33042281"],"is_preprint":false},{"year":2020,"finding":"IFNB/interferon-β induces expression of miR-1, which reduces TBC1D15 levels, thereby decreasing Rab7 activity and stimulating autophagy; this MIR1-TBC1D15-RAB7 pathway is conserved from humans to C. elegans and its disruption leads to late-stage autophagic flux block and α-synuclein accumulation.","method":"MicroRNA expression manipulation, TBC1D15 knockdown/overexpression, autophagy flux assays, cross-species genetic conservation analysis","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2–3 — genetic pathway placement with functional readout across species, mechanism supported by prior in vitro work","pmids":["31958036"],"is_preprint":false},{"year":2022,"finding":"TBC1D15 directly interacts with Drp1 through its C-terminal 574–624 domain and recruits Drp1 to mitochondria-lysosome contact sites to drive asymmetrical mitochondrial fission. Deletion of this domain (Δ574-624) or interference with TBC1D15–Drp1 interaction abrogates asymmetrical fission and mitochondrial function. TBC1D15 also operates via a Fis1/RAB7 cascade to regulate contact untethering.","method":"Cardiac-specific knockin/knockout mouse models, time-lapse confocal microscopy, domain-deletion and point-mutant rescue experiments (R400K, Δ231-240, Δ574-624), co-immunoprecipitation","journal":"Metabolism: clinical and experimental","confidence":"High","confidence_rationale":"Tier 2 — domain-mapping with multiple mutants, in vivo genetic models, and live imaging; Drp1 interaction confirmed by co-IP with functional domain delineated","pmids":["35680100"],"is_preprint":false},{"year":2023,"finding":"Following lysosomal membrane damage, LIMP2 acts as a lysophagy receptor binding ATG8, which in turn recruits TBC1D15 to damaged lysosomes. TBC1D15 then interacts with ATG8 proteins and acts as a scaffold to assemble the autophagic lysosomal reformation (ALR) machinery (dynamin-2, kinesin-5B, clathrin), promoting lysosomal tubule formation and dynamin-2-dependent scission for membrane regeneration.","method":"Proximity-labeling proteomics, co-immunoprecipitation, high-resolution fluorescence microscopy, siRNA knockdown with lysosomal morphology and function readouts","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 — proximity proteomics plus reciprocal co-IPs plus live imaging in a mechanistically coherent pathway, high-profile journal","pmids":["37024685"],"is_preprint":false},{"year":2023,"finding":"TBC1D15 interacts with DNA-PKcs at the segment 594–624 of TBC1D15 (identified by LC-MS/MS and co-IP) and promotes cytosolic accumulation of DNA-PKcs; deletion of this segment (Δ594-624) abolishes the ability of TBC1D15 to foster DNA-PKcs cytosolic retention and doxorubicin-induced DNA damage.","method":"LC-tandem mass spectrometry, co-immunoprecipitation, domain-deletion mutagenesis, cardiac-specific knockout/knockin mouse models, DNA damage assays","journal":"Acta pharmaceutica Sinica. B","confidence":"Medium","confidence_rationale":"Tier 2 — MS-identified interaction confirmed by co-IP with domain-deletion functional rescue, single lab","pmids":["38045047"],"is_preprint":false},{"year":2013,"finding":"Drosophila Tbc1d15-17 (ortholog of mammalian TBC1D15/Rab7-GAP) is required for normal synaptic bouton number and NMJ length; loss-of-function or presynaptic knockdown causes synaptic overgrowth. Postsynaptic knockdown disrupts Dlg scaffold distribution and GluRIIA levels. Presynaptic overexpression of constitutively active Rab7 phenocopies Tbc1d15-17 loss, while dominant-negative Rab7 has the opposite effect, placing Tbc1d15-17 upstream of Rab7 in synaptic growth control.","method":"Drosophila loss-of-function genetics, tissue-specific RNAi knockdown, constitutively active/dominant-negative Rab7 epistasis, immunofluorescence microscopy at NMJ","journal":"Molecules and cells","confidence":"Medium","confidence_rationale":"Tier 2 — genetic epistasis with Rab7 in ortholog model organism, multiple tissue-specific manipulations","pmids":["23812537"],"is_preprint":false},{"year":2017,"finding":"TBC1D15 knockdown rescues nigericin-induced mitochondrial fission and restores STING pathway activation, whereas Drp1 knockdown rescues fission but does not restore STING activity. This places TBC1D15—but not Drp1—as the specific mediator through which inflammasome-activating signals curtail STING pathway activity.","method":"siRNA knockdown of TBC1D15 or Drp1, mitochondrial morphology imaging, STING pathway reporter assays (IFN-β, ISG56, TBK1, IRF3 activation)","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2–3 — genetic epistasis by differential KD rescue with functional pathway readout, single lab","pmids":["28729291"],"is_preprint":false},{"year":2018,"finding":"TBC1D15 regulates GLUT4 translocation and glucose uptake; CRISPR/Cas9 knockout of TBC1D15 reduces 2-NBDG uptake, decreases total GLUT4 protein, and causes GLUT4 to accumulate in Rab7-positive late endosomes/lysosomes, consistent with TBC1D15's Rab7 GAP activity controlling late endosomal GLUT4 trafficking.","method":"CRISPR/Cas9 knockout, fluorescent glucose analog uptake assay (2-NBDG), immunofluorescence co-localization of GLUT4 and Rab7/LAMP1","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2–3 — clean KO with defined transport phenotype and mechanistic co-localization, single lab","pmids":["30316925"],"is_preprint":false},{"year":2024,"finding":"TBC1D15 functions as a GAP for Arl4D (a Ras-family GTPase) in addition to Rab7; it interacts with Arl4D through the TBC domain and promotes GTP hydrolysis of Arl4D. Knockdown of TBC1D15 increases Arl4D-GTP levels and decreases Arl4D mitochondrial translocation under serum starvation, placing TBC1D15 as an upstream regulator of Arl4D mitochondrial targeting.","method":"Co-immunoprecipitation, in vitro GAP activity assay, TBC domain interaction mapping, TBC1D15 knockdown with Arl4D-GTP effector pull-down and mitochondrial localization readout","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 1–2 — in vitro GAP assay with domain mapping and KD phenotype, but single lab","pmids":["41709823"],"is_preprint":false},{"year":2024,"finding":"TBC1D15 stabilizes NOTCH1 by blocking CDK8/CDK19-mediated phosphorylation of the NOTCH1 PEST phosphodegron, thereby preventing FBW7-mediated ubiquitin-dependent degradation. The TBC1D15-FIS1 interaction recruits NOTCH1 to the mitochondrial outer membrane in the perinuclear region. TBC1D15 also binds NUMB isoform 5 (lacking Ser phosphorylation sites) and relocalizes NUMB5 to mitochondria.","method":"Co-immunoprecipitation, ChIP-seq, domain-interaction mapping, CDK8 kinase assays, in vivo triple-knockout mouse model (hepatocyte-specific Tbc1d15/Notch1/Notch2), PDX tumor models","journal":"Experimental & molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — multiple interaction assays with mechanistic kinase pathway placement and in vivo genetic validation, single lab","pmids":["38409448"],"is_preprint":false},{"year":2023,"finding":"FIS1 contains a conserved noncanonical 'SKY insert' (S45-K46-Y47) in its first TPR repeat that governs TBC1D15 and DRP1 recruitment to mitochondria. Deletion of the SKY insert (ΔSKY) reduces mitochondrial TBC1D15 and DRP1 recruitment despite DRP1 still co-immunoprecipitating with ΔSKY FIS1, demonstrating that the insert is required for productive mitochondrial fission complex assembly.","method":"Structure-based sequence alignment, FIS1 variant expression in HCT116 cells, co-immunoprecipitation, fluorescence microscopy of YFP-TBC1D15 recruitment, mitochondrial morphology analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — structure-guided mutagenesis with co-IP and localization readouts, single lab","pmids":["37777154"],"is_preprint":false},{"year":2025,"finding":"TBC1D15 is translocated to the mitochondrial membrane in hepatocytes upon ethanol exposure, where it recruits PLIN5 through its 10–180 aa domain, promoting mitochondria-lipid droplet contacts. This interaction facilitates PKA-induced nuclear translocation of PLIN5 and upregulates PPARα/PGC1α/CPT1α, enhancing mitochondrial fatty acid β-oxidation; PKA inhibition nullifies these effects.","method":"Hepatocyte-specific TBC1D15 overexpression mouse model, co-immunoprecipitation, domain-mapping (10–180 aa), immunofluorescence microscopy, PKA inhibitor experiments, transmission electron microscopy","journal":"Metabolism: clinical and experimental","confidence":"Medium","confidence_rationale":"Tier 2–3 — domain-mapped interaction with mechanistic pharmacological rescue, single lab","pmids":["40334909"],"is_preprint":false},{"year":2024,"finding":"Tbc1d15 knockdown in vivo activates autophagy, reduces α-synuclein-mediated neurotoxicity, and improves motor performance in a mouse model of Parkinson's disease, consistent with TBC1D15 acting as an inhibitor of autophagic flux via Rab7 GAP activity.","method":"In vivo Tbc1d15 knockdown (mouse), autophagy flux assays, α-synuclein aggregate quantification, motor behavior testing","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 2–3 — in vivo KD with functional readout but preprint, single lab, no peer review","pmids":["bio_10.1101_2024.10.01.616109"],"is_preprint":true}],"current_model":"TBC1D15 is a multifunctional TBC-domain protein that acts primarily as a Rab7 GTPase-activating protein (GAP) to inactivate Rab7 and thereby control late endosome/lysosome morphology, mitophagy flux, and autophagic lysosomal reformation; it is recruited to the mitochondrial outer membrane by direct binding to Fis1, where it also interacts with Drp1 (via its C-terminal 574–624 domain) to drive asymmetrical mitochondrial fission, regulates mitochondria-lysosome contact duration, and in the nucleus-cytoplasm axis stabilizes oncoproteins such as NOTCH1 by blocking CDK8-mediated phosphodegron phosphorylation, while additionally functioning as a GAP for Arl4D and as a scaffold for lysosomal membrane regeneration downstream of ATG8 and LIMP2."},"narrative":{"teleology":[{"year":2010,"claim":"Establishing that TBC1D15 is a selective Rab7 GAP answered the fundamental question of which TBC protein controls late endosome/lysosome identity, linking its activity to lysosomal morphology and cell survival.","evidence":"Effector pull-down (RILP–Rab7-GTP), lysosome imaging, selectivity controls against Rab4/5/11 in mammalian cells","pmids":["20363736"],"confidence":"High","gaps":["No structural basis for Rab7 selectivity at this stage","Upstream regulators of TBC1D15 recruitment unknown"]},{"year":2012,"claim":"Identifying Fis1 as the mitochondrial receptor for TBC1D15 revealed how a cytosolic Rab-GAP is targeted to the mitochondrial outer membrane, establishing a previously unrecognized connection between endolysosomal Rab7 signaling and mitochondrial dynamics.","evidence":"Bacterially reconstituted direct Fis1–TBC1D15 complex, reciprocal co-IP from HeLa cells, fluorescence relocalization, siRNA knockdown morphology","pmids":["23077178"],"confidence":"High","gaps":["Binding interface on Fis1 not mapped at residue level","Whether Rab7 GAP activity is required for the mitochondrial morphology phenotype untested"]},{"year":2013,"claim":"Work in Drosophila demonstrated that Rab7-GAP control of endolysosomal trafficking by TBC1D15 orthologs extends to synaptic growth, while mammalian studies revealed additional non-GAP functions including Numb/p53 complex disruption and RhoA cortical regulation.","evidence":"Drosophila loss-of-function/Rab7 epistasis at NMJ; mammalian AP-MS identifying Numb interaction; siRNA-mediated RhoA activation and membrane blebbing phenotype","pmids":["23812537","23468968","24337944"],"confidence":"Medium","gaps":["RhoA regulation mechanism (direct or indirect) not resolved","Numb interaction domain overlap with GAP domain not tested","Synaptic overgrowth phenotype not confirmed in mammalian neurons"]},{"year":2017,"claim":"Crystal structures of the TBC1D15 GAP domain combined with active-site mutagenesis established the dual-finger catalytic mechanism, while functional studies positioned TBC1D15 as a specific mediator coupling inflammasome signals to STING pathway suppression.","evidence":"X-ray crystallography (2.5–2.8 Å), Arg/Gln catalytic mutants; siRNA epistasis separating TBC1D15 from Drp1 in STING regulation","pmids":["28168758","28729291"],"confidence":"High","gaps":["No Rab7-bound co-crystal structure","STING pathway placement relies on knockdown epistasis without direct binding evidence"]},{"year":2018,"claim":"CRISPR knockout of TBC1D15 showed that its Rab7 GAP activity controls GLUT4 trafficking, with loss causing GLUT4 accumulation in Rab7-positive late endosomes and reduced glucose uptake.","evidence":"CRISPR/Cas9 KO, fluorescent glucose analog uptake, GLUT4–Rab7/LAMP1 co-localization","pmids":["30316925"],"confidence":"Medium","gaps":["Insulin-stimulated GLUT4 exocytosis not tested","Rescue with GAP-dead mutant not performed"]},{"year":2019,"claim":"Placing Annexin A6 upstream of TBC1D15 as a stimulator of its Rab7-GAP activity linked TBC1D15 to cholesterol export pathways at late endosome–ER membrane contact sites, expanding its role beyond organelle morphology.","evidence":"Co-IP, Rab7-GTP effector pull-down, live imaging, EM of membrane contacts in NPC1 mutant cells","pmids":["31664461"],"confidence":"Medium","gaps":["Direct AnxA6–TBC1D15 binding not reconstituted in vitro","Cholesterol flux measurements indirect"]},{"year":2020,"claim":"Studies demonstrated that both the Fis1-binding and Rab7-GAP domains of TBC1D15 are independently required for regulating mitochondria–lysosome contacts and mitophagy flux, while a conserved miR-1–TBC1D15–Rab7 axis was shown to control autophagic clearance of α-synuclein.","evidence":"Domain-mutation rescue experiments with live imaging and cardiac functional assessment; miR-1 manipulation with cross-species genetic analysis (human to C. elegans)","pmids":["33042281","31958036"],"confidence":"High","gaps":["Stoichiometry of Fis1–TBC1D15 complex at contacts not determined","miR-1 regulation in non-neuronal contexts not characterized"]},{"year":2022,"claim":"Identification of the C-terminal 574–624 domain as the Drp1-binding interface resolved how TBC1D15 drives asymmetrical mitochondrial fission at mitochondria–lysosome contact sites, distinguishing this function from its Rab7-GAP and Fis1-binding activities.","evidence":"Cardiac-specific knockin/knockout mice, domain-deletion/point-mutant rescue, time-lapse confocal microscopy, co-IP","pmids":["35680100"],"confidence":"High","gaps":["Direct structural basis of TBC1D15–Drp1 interaction not resolved","Whether asymmetric fission occurs in non-cardiac tissues untested"]},{"year":2023,"claim":"Discovery that LIMP2–ATG8 recruits TBC1D15 to damaged lysosomes for autophagic lysosomal reformation recast TBC1D15 as a scaffolding platform for membrane regeneration machinery (dynamin-2, kinesin-5B, clathrin), while parallel work mapped the Fis1 SKY-insert as the determinant of productive TBC1D15/DRP1 mitochondrial recruitment.","evidence":"Proximity-labeling proteomics, reciprocal co-IPs, live imaging of lysosomal tubulation; structure-guided FIS1 mutagenesis with YFP-TBC1D15 recruitment assay","pmids":["37024685","37777154"],"confidence":"High","gaps":["Order of scaffold assembly (dynamin-2 vs. kinesin-5B recruitment) not resolved","Whether ALR scaffolding requires TBC1D15 GAP activity is untested"]},{"year":2024,"claim":"Expanding its substrate repertoire, TBC1D15 was shown to function as a GAP for Arl4D, regulating Arl4D mitochondrial translocation, while mechanistic work demonstrated that TBC1D15 stabilizes NOTCH1 by blocking CDK8-mediated phosphodegron phosphorylation and interacts with DNA-PKcs to promote its cytosolic retention.","evidence":"In vitro Arl4D GAP assay with domain mapping; CDK8 kinase assays and triple-KO hepatocyte mouse model for NOTCH1; LC-MS/MS identification and domain-deletion for DNA-PKcs interaction","pmids":["41709823","38409448","38045047"],"confidence":"Medium","gaps":["Arl4D GAP activity not independently confirmed","Whether NOTCH1 stabilization requires Rab7 GAP activity unknown","DNA-PKcs cytosolic retention mechanism not structurally characterized"]},{"year":2025,"claim":"TBC1D15 was found to recruit PLIN5 to mitochondria via its N-terminal 10–180 domain, promoting mitochondria–lipid droplet contacts and PKA-dependent PLIN5 nuclear translocation that upregulates fatty acid β-oxidation genes, revealing a new organelle contact function.","evidence":"Hepatocyte-specific TBC1D15 overexpression mouse model, co-IP, domain-mapping, PKA inhibitor experiments, TEM","pmids":["40334909"],"confidence":"Medium","gaps":["Direct TBC1D15–PLIN5 binding not reconstituted with purified proteins","Whether ethanol-induced mitochondrial translocation of TBC1D15 requires Fis1 not tested","Relationship to TBC1D15's Rab7 GAP activity in this context unclear"]},{"year":null,"claim":"Key unresolved questions include how TBC1D15's multiple binding interfaces (Fis1, Drp1, ATG8, PLIN5, DNA-PKcs, NOTCH1) are coordinated or compete, whether its GAP activity toward Rab7 versus Arl4D is differentially regulated, and the structural basis of its scaffold functions in ALR and mitochondrial fission.","evidence":"","pmids":[],"confidence":"Low","gaps":["No full-length TBC1D15 structure available","Competition or cooperativity among binding partners not systematically tested","Tissue-specific regulation of TBC1D15 functions poorly understood"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[1,2,14]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2,5,6,14]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[9,15,17]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,6,8,16,17]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[1,6,9]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[5,13]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[7,9]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,6,8,9]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,5,13]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[15]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[17]}],"complexes":["Fis1-TBC1D15-Drp1 mitochondrial fission complex","LIMP2-ATG8-TBC1D15 ALR scaffold"],"partners":["FIS1","RAB7A","DRP1","LIMP2","ANXA6","PLIN5","ARL4D","NOTCH1"],"other_free_text":[]},"mechanistic_narrative":"TBC1D15 is a Rab7 GTPase-activating protein and multifunctional scaffold that integrates late endosome/lysosome dynamics, mitochondrial fission, and autophagic membrane recycling. Its TBC domain catalyzes GTP hydrolysis on Rab7 (and Arl4D) via a conserved dual-finger mechanism, thereby controlling lysosomal size, GLUT4 trafficking through the late endosomal compartment, and autophagy flux [PMID:20363736, PMID:28168758, PMID:30316925, PMID:41709823]. TBC1D15 is recruited to the mitochondrial outer membrane by direct binding to Fis1 (through a conserved SKY-insert-dependent interface), where it further engages Drp1 via its C-terminal 574–624 domain to drive asymmetrical mitochondrial fission and regulate mitochondria–lysosome contact duration [PMID:23077178, PMID:35680100, PMID:37777154]. Following lysosomal damage, TBC1D15 is recruited via LIMP2–ATG8 and scaffolds the autophagic lysosomal reformation machinery (dynamin-2, kinesin-5B, clathrin) for membrane regeneration, and at the mitochondrial surface it stabilizes NOTCH1 by blocking CDK8-mediated phosphodegron phosphorylation [PMID:37024685, PMID:38409448]."},"prefetch_data":{"uniprot":{"accession":"Q8TC07","full_name":"TBC1 domain family member 15","aliases":["GTPase-activating protein RAB7","GAP for RAB7","Rab7-GAP"],"length_aa":691,"mass_kda":79.5,"function":"Acts as a GTPase activating protein for RAB7A. Does not act on RAB4, RAB5 or RAB6 (By similarity)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q8TC07/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TBC1D15","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TBC1D15","total_profiled":1310},"omim":[{"mim_id":"620377","title":"ARMADILLO REPEAT-CONTAINING PROTEIN 12; ARMC12","url":"https://www.omim.org/entry/620377"},{"mim_id":"614166","title":"MYOPIA 20, AUTOSOMAL DOMINANT; MYP20","url":"https://www.omim.org/entry/614166"},{"mim_id":"612662","title":"TBC1 DOMAIN FAMILY, MEMBER 15; TBC1D15","url":"https://www.omim.org/entry/612662"},{"mim_id":"602298","title":"RAS-ASSOCIATED PROTEIN RAB7A; RAB7A","url":"https://www.omim.org/entry/602298"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mitochondria","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TBC1D15"},"hgnc":{"alias_symbol":["FLJ12085","DKFZp761D0223"],"prev_symbol":[]},"alphafold":{"accession":"Q8TC07","domains":[{"cath_id":"2.30.29.230","chopping":"11-56_126-196","consensus_level":"high","plddt":79.738,"start":11,"end":196},{"cath_id":"1.10.472.80","chopping":"276-328_488-632","consensus_level":"medium","plddt":86.5547,"start":276,"end":632},{"cath_id":"1.10.8.270","chopping":"348-484","consensus_level":"high","plddt":95.5133,"start":348,"end":484}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TC07","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TC07-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TC07-F1-predicted_aligned_error_v6.png","plddt_mean":70.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TBC1D15","jax_strain_url":"https://www.jax.org/strain/search?query=TBC1D15"},"sequence":{"accession":"Q8TC07","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8TC07.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8TC07/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TC07"}},"corpus_meta":[{"pmid":"23077178","id":"PMC_23077178","title":"Fis1 acts as a mitochondrial recruitment factor for TBC1D15 that is involved in regulation of mitochondrial morphology.","date":"2012","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/23077178","citation_count":122,"is_preprint":false},{"pmid":"33042281","id":"PMC_33042281","title":"TBC1D15/RAB7-regulated mitochondria-lysosome interaction confers cardioprotection against acute myocardial infarction-induced cardiac injury.","date":"2020","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/33042281","citation_count":104,"is_preprint":false},{"pmid":"20363736","id":"PMC_20363736","title":"Differential effects of TBC1D15 and mammalian Vps39 on Rab7 activation state, lysosomal morphology, and growth factor dependence.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20363736","citation_count":101,"is_preprint":false},{"pmid":"37024685","id":"PMC_37024685","title":"A lysosome membrane regeneration pathway depends on TBC1D15 and autophagic lysosomal reformation proteins.","date":"2023","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/37024685","citation_count":63,"is_preprint":false},{"pmid":"31664461","id":"PMC_31664461","title":"Annexin A6 modulates TBC1D15/Rab7/StARD3 axis to control endosomal cholesterol export in NPC1 cells.","date":"2019","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/31664461","citation_count":60,"is_preprint":false},{"pmid":"35680100","id":"PMC_35680100","title":"TBC1D15-Drp1 interaction-mediated mitochondrial homeostasis confers cardioprotection against myocardial ischemia/reperfusion injury.","date":"2022","source":"Metabolism: clinical and experimental","url":"https://pubmed.ncbi.nlm.nih.gov/35680100","citation_count":53,"is_preprint":false},{"pmid":"28729291","id":"PMC_28729291","title":"Stimulator of IFN genes-mediated DNA-sensing pathway is suppressed by NLRP3 agonists and regulated by mitofusin 1 and TBC1D15, mitochondrial dynamics mediators.","date":"2017","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/28729291","citation_count":25,"is_preprint":false},{"pmid":"23468968","id":"PMC_23468968","title":"The TBC1D15 oncoprotein controls stem cell self-renewal through destabilization of the Numb-p53 complex.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23468968","citation_count":22,"is_preprint":false},{"pmid":"38045047","id":"PMC_38045047","title":"TBC1D15 deficiency protects against doxorubicin cardiotoxicity via inhibiting DNA-PKcs cytosolic retention and DNA damage.","date":"2023","source":"Acta pharmaceutica Sinica. 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blebbing.","date":"2013","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24337944","citation_count":10,"is_preprint":false},{"pmid":"39390030","id":"PMC_39390030","title":"TBC1D15-regulated mitochondria-lysosome membrane contact exerts neuroprotective effects by alleviating mitochondrial calcium overload in seizure.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39390030","citation_count":8,"is_preprint":false},{"pmid":"37777154","id":"PMC_37777154","title":"A conserved, noncanonical insert in FIS1 mediates TBC1D15 and DRP1 recruitment for mitochondrial fission.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37777154","citation_count":7,"is_preprint":false},{"pmid":"40334909","id":"PMC_40334909","title":"TBC1D15 protects alcohol-induced liver injury in female mice through PLIN5-mediated mitochondrial and lipid droplet 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pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/38749178","citation_count":5,"is_preprint":false},{"pmid":"39740704","id":"PMC_39740704","title":"The role of TBC1D15 in sepsis-induced acute lung injury: Regulation of mitochondrial homeostasis and mitophagy.","date":"2024","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/39740704","citation_count":5,"is_preprint":false},{"pmid":"38409448","id":"PMC_38409448","title":"NOTCH localizes to mitochondria through the TBC1D15-FIS1 interaction and is stabilized via blockade of E3 ligase and CDK8 recruitment to reprogram tumor-initiating cells.","date":"2024","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38409448","citation_count":5,"is_preprint":false},{"pmid":"38110073","id":"PMC_38110073","title":"Upregulation of mitochondrial PGK1 by ROS-TBC1D15 pathway promotes neuronal death after oxygen-glucose deprivation/reoxygenation injury.","date":"2023","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/38110073","citation_count":3,"is_preprint":false},{"pmid":"30755162","id":"PMC_30755162","title":"A fragment activity assay reveals the key residues of TBC1D15 GTPase-activating protein (GAP) in Chiloscyllium plagiosum.","date":"2019","source":"BMC molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/30755162","citation_count":2,"is_preprint":false},{"pmid":"41360698","id":"PMC_41360698","title":"Songorine inhibits mitophagy in chronic heart failure via the TBC1D15/Fis1/Rab7A pathway.","date":"2025","source":"British journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41360698","citation_count":0,"is_preprint":false},{"pmid":"41709823","id":"PMC_41709823","title":"TBC1D15 functions as an Arl4D GAP and promotes the mitochondrial translocation of Arl4D for organelle homeostasis.","date":"2026","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/41709823","citation_count":0,"is_preprint":false},{"pmid":"41607534","id":"PMC_41607534","title":"Case Report: Pediatric AML with TBC1D15::RAB21 fusion and FLT3-ITD/NPM1 co-mutation: diagnostic pitfalls in morphologic mimicry of acute promyelocytic leukemia.","date":"2026","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41607534","citation_count":0,"is_preprint":false},{"pmid":"40727815","id":"PMC_40727815","title":"TBC1D15 Expression Indicates the Toxicity of Gold Nanoparticles on Mitochondria in PC-12 Cells.","date":"2025","source":"ACS omega","url":"https://pubmed.ncbi.nlm.nih.gov/40727815","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.07.674666","title":"Astrocytes mobilize a broader repertoire of lysosomal repair mechanisms than neurons","date":"2025-09-08","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.07.674666","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.01.616109","title":"Tbc1d15 knockdown<i>in vivo</i>alleviates α-synuclein-induced neurotoxicity by promoting autophagy","date":"2024-10-03","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.01.616109","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":16457,"output_tokens":5236,"usd":0.063955},"stage2":{"model":"claude-opus-4-6","input_tokens":8815,"output_tokens":3464,"usd":0.196013},"total_usd":0.259968,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"Fis1 acts as a mitochondrial receptor that directly recruits TBC1D15 to the mitochondrial outer membrane; bacterially expressed Fis1 and TBC1D15 form a direct and stable complex, and TBC1D15 (normally cytoplasmic) relocalizes to mitochondria when co-expressed with Fis1. Knockdown of TBC1D15 induces highly developed mitochondrial network structures, placing TBC1D15 in regulation of mitochondrial morphology independently of Drp1.\",\n      \"method\": \"Co-immunoprecipitation from HeLa cell extracts, bacterial reconstitution of direct complex, fluorescence microscopy of co-expressed proteins, siRNA knockdown with morphological readout\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct binding reconstituted in vitro plus reciprocal co-IP plus localization experiment with functional consequence; replicated concept across multiple methods in same study\",\n      \"pmids\": [\"23077178\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"TBC1D15 functions as a Rab7 GTPase-activating protein (GAP) in cells, reducing Rab7 binding to its effector RILP (measured by effector pull-down assay), fragmenting lysosomes, and conferring resistance to growth factor withdrawal-induced cell death. TBC1D15 GAP activity is selective for Rab7 and does not affect Rab4-, Rab5-, or Rab11-dependent processes.\",\n      \"method\": \"Effector pull-down assay (RILP-Rab7-GTP binding), lysosomal morphology imaging, cell death assays, transferrin recycling assay as selectivity control\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — cell-based GAP activity assay with multiple orthogonal readouts (effector binding, organelle morphology, cell survival, selectivity controls); highly cited foundational study\",\n      \"pmids\": [\"20363736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structures of the TBC1D15 GAP domain (shark and pig orthologs) were solved to 2.8 Å and 2.5 Å resolution, revealing conservation with but distinct variations from yeast Gyp1p and TBC1D1. Active-site mutagenesis (Arg→Ala or Lys) of the catalytic arginine and glutamine residues abolishes GAP activity, confirming the dual-finger catalytic mechanism.\",\n      \"method\": \"X-ray crystallography, in vitro GAP activity assay, active-site mutagenesis\",\n      \"journal\": \"Protein science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure combined with mutagenesis and in vitro enzymatic assay\",\n      \"pmids\": [\"28168758\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"TBC1D15 is identified as a Numb-associated protein by large-scale affinity purification/mass spectrometry; its amino-terminal domain disengages p53 from the Numb–p53 complex, triggering p53 proteolysis and promoting stem cell self-renewal. TBC1D15 protein levels are reduced by autophagy-mediated degradation upon nutrient deprivation.\",\n      \"method\": \"Affinity purification and tandem mass spectrometry, co-immunoprecipitation, domain-mapping with deletion constructs, p53 stability assays, autophagy inhibitor experiments\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — MS-identified interaction confirmed by co-IP with domain mapping and functional readout, single lab\",\n      \"pmids\": [\"23468968\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Depletion of TBC1D15 in HeLa cells induces RhoA activation and membrane blebbing, which is abolished by RhoA signaling inhibitors. TBC1D15 is also required for proper accumulation of RhoA at the equatorial cortex during cytokinesis, establishing a role for TBC1D15 in RhoA-mediated cortical dynamics.\",\n      \"method\": \"siRNA knockdown, RhoA activity assay (pull-down), pharmacological inhibition of RhoA, fluorescence microscopy of cytokinesis\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — KD with defined phenotypic readout and pathway placement via pharmacological rescue, single lab\",\n      \"pmids\": [\"24337944\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Annexin A6 promotes Rab7 inactivation by stimulating TBC1D15 (Rab7-GAP) activity; AnxA6 depletion in NPC1 mutant cells leads to Rab7 activation, peripheral redistribution of late endosomes, and enhanced cholesterol export to lipid droplets via StARD3-dependent membrane contact sites between late endosomes and ER.\",\n      \"method\": \"Co-immunoprecipitation, effector pull-down (Rab7-GTP), fluorescence live-cell imaging, electron microscopy of membrane contact sites, ACAT inhibitor assays\",\n      \"journal\": \"Cellular and molecular life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods placing TBC1D15 in an AnxA6–Rab7 axis, single lab\",\n      \"pmids\": [\"31664461\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TBC1D15 regulates mitochondria-lysosome contacts through both its Fis1-binding domain and its Rab7 GAP domain; overexpression loosens abnormal mitochondria-lysosome contacts, restores lysosomal size and function, and rescues mitophagy flux after myocardial infarction. Interference with either domain individually abrogates the beneficial effects.\",\n      \"method\": \"Transmission electron microscopy, live-cell time-lapse imaging, adenoviral overexpression, domain-mutation rescue experiments, mitophagy flux assays (fluorescence and western blotting), cardiac functional assessment\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods with domain-specific mutant controls, in vitro and in vivo validation\",\n      \"pmids\": [\"33042281\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"IFNB/interferon-β induces expression of miR-1, which reduces TBC1D15 levels, thereby decreasing Rab7 activity and stimulating autophagy; this MIR1-TBC1D15-RAB7 pathway is conserved from humans to C. elegans and its disruption leads to late-stage autophagic flux block and α-synuclein accumulation.\",\n      \"method\": \"MicroRNA expression manipulation, TBC1D15 knockdown/overexpression, autophagy flux assays, cross-species genetic conservation analysis\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — genetic pathway placement with functional readout across species, mechanism supported by prior in vitro work\",\n      \"pmids\": [\"31958036\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TBC1D15 directly interacts with Drp1 through its C-terminal 574–624 domain and recruits Drp1 to mitochondria-lysosome contact sites to drive asymmetrical mitochondrial fission. Deletion of this domain (Δ574-624) or interference with TBC1D15–Drp1 interaction abrogates asymmetrical fission and mitochondrial function. TBC1D15 also operates via a Fis1/RAB7 cascade to regulate contact untethering.\",\n      \"method\": \"Cardiac-specific knockin/knockout mouse models, time-lapse confocal microscopy, domain-deletion and point-mutant rescue experiments (R400K, Δ231-240, Δ574-624), co-immunoprecipitation\",\n      \"journal\": \"Metabolism: clinical and experimental\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — domain-mapping with multiple mutants, in vivo genetic models, and live imaging; Drp1 interaction confirmed by co-IP with functional domain delineated\",\n      \"pmids\": [\"35680100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Following lysosomal membrane damage, LIMP2 acts as a lysophagy receptor binding ATG8, which in turn recruits TBC1D15 to damaged lysosomes. TBC1D15 then interacts with ATG8 proteins and acts as a scaffold to assemble the autophagic lysosomal reformation (ALR) machinery (dynamin-2, kinesin-5B, clathrin), promoting lysosomal tubule formation and dynamin-2-dependent scission for membrane regeneration.\",\n      \"method\": \"Proximity-labeling proteomics, co-immunoprecipitation, high-resolution fluorescence microscopy, siRNA knockdown with lysosomal morphology and function readouts\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — proximity proteomics plus reciprocal co-IPs plus live imaging in a mechanistically coherent pathway, high-profile journal\",\n      \"pmids\": [\"37024685\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TBC1D15 interacts with DNA-PKcs at the segment 594–624 of TBC1D15 (identified by LC-MS/MS and co-IP) and promotes cytosolic accumulation of DNA-PKcs; deletion of this segment (Δ594-624) abolishes the ability of TBC1D15 to foster DNA-PKcs cytosolic retention and doxorubicin-induced DNA damage.\",\n      \"method\": \"LC-tandem mass spectrometry, co-immunoprecipitation, domain-deletion mutagenesis, cardiac-specific knockout/knockin mouse models, DNA damage assays\",\n      \"journal\": \"Acta pharmaceutica Sinica. B\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — MS-identified interaction confirmed by co-IP with domain-deletion functional rescue, single lab\",\n      \"pmids\": [\"38045047\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Drosophila Tbc1d15-17 (ortholog of mammalian TBC1D15/Rab7-GAP) is required for normal synaptic bouton number and NMJ length; loss-of-function or presynaptic knockdown causes synaptic overgrowth. Postsynaptic knockdown disrupts Dlg scaffold distribution and GluRIIA levels. Presynaptic overexpression of constitutively active Rab7 phenocopies Tbc1d15-17 loss, while dominant-negative Rab7 has the opposite effect, placing Tbc1d15-17 upstream of Rab7 in synaptic growth control.\",\n      \"method\": \"Drosophila loss-of-function genetics, tissue-specific RNAi knockdown, constitutively active/dominant-negative Rab7 epistasis, immunofluorescence microscopy at NMJ\",\n      \"journal\": \"Molecules and cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with Rab7 in ortholog model organism, multiple tissue-specific manipulations\",\n      \"pmids\": [\"23812537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TBC1D15 knockdown rescues nigericin-induced mitochondrial fission and restores STING pathway activation, whereas Drp1 knockdown rescues fission but does not restore STING activity. This places TBC1D15—but not Drp1—as the specific mediator through which inflammasome-activating signals curtail STING pathway activity.\",\n      \"method\": \"siRNA knockdown of TBC1D15 or Drp1, mitochondrial morphology imaging, STING pathway reporter assays (IFN-β, ISG56, TBK1, IRF3 activation)\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — genetic epistasis by differential KD rescue with functional pathway readout, single lab\",\n      \"pmids\": [\"28729291\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TBC1D15 regulates GLUT4 translocation and glucose uptake; CRISPR/Cas9 knockout of TBC1D15 reduces 2-NBDG uptake, decreases total GLUT4 protein, and causes GLUT4 to accumulate in Rab7-positive late endosomes/lysosomes, consistent with TBC1D15's Rab7 GAP activity controlling late endosomal GLUT4 trafficking.\",\n      \"method\": \"CRISPR/Cas9 knockout, fluorescent glucose analog uptake assay (2-NBDG), immunofluorescence co-localization of GLUT4 and Rab7/LAMP1\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — clean KO with defined transport phenotype and mechanistic co-localization, single lab\",\n      \"pmids\": [\"30316925\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TBC1D15 functions as a GAP for Arl4D (a Ras-family GTPase) in addition to Rab7; it interacts with Arl4D through the TBC domain and promotes GTP hydrolysis of Arl4D. Knockdown of TBC1D15 increases Arl4D-GTP levels and decreases Arl4D mitochondrial translocation under serum starvation, placing TBC1D15 as an upstream regulator of Arl4D mitochondrial targeting.\",\n      \"method\": \"Co-immunoprecipitation, in vitro GAP activity assay, TBC domain interaction mapping, TBC1D15 knockdown with Arl4D-GTP effector pull-down and mitochondrial localization readout\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro GAP assay with domain mapping and KD phenotype, but single lab\",\n      \"pmids\": [\"41709823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TBC1D15 stabilizes NOTCH1 by blocking CDK8/CDK19-mediated phosphorylation of the NOTCH1 PEST phosphodegron, thereby preventing FBW7-mediated ubiquitin-dependent degradation. The TBC1D15-FIS1 interaction recruits NOTCH1 to the mitochondrial outer membrane in the perinuclear region. TBC1D15 also binds NUMB isoform 5 (lacking Ser phosphorylation sites) and relocalizes NUMB5 to mitochondria.\",\n      \"method\": \"Co-immunoprecipitation, ChIP-seq, domain-interaction mapping, CDK8 kinase assays, in vivo triple-knockout mouse model (hepatocyte-specific Tbc1d15/Notch1/Notch2), PDX tumor models\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple interaction assays with mechanistic kinase pathway placement and in vivo genetic validation, single lab\",\n      \"pmids\": [\"38409448\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FIS1 contains a conserved noncanonical 'SKY insert' (S45-K46-Y47) in its first TPR repeat that governs TBC1D15 and DRP1 recruitment to mitochondria. Deletion of the SKY insert (ΔSKY) reduces mitochondrial TBC1D15 and DRP1 recruitment despite DRP1 still co-immunoprecipitating with ΔSKY FIS1, demonstrating that the insert is required for productive mitochondrial fission complex assembly.\",\n      \"method\": \"Structure-based sequence alignment, FIS1 variant expression in HCT116 cells, co-immunoprecipitation, fluorescence microscopy of YFP-TBC1D15 recruitment, mitochondrial morphology analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — structure-guided mutagenesis with co-IP and localization readouts, single lab\",\n      \"pmids\": [\"37777154\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TBC1D15 is translocated to the mitochondrial membrane in hepatocytes upon ethanol exposure, where it recruits PLIN5 through its 10–180 aa domain, promoting mitochondria-lipid droplet contacts. This interaction facilitates PKA-induced nuclear translocation of PLIN5 and upregulates PPARα/PGC1α/CPT1α, enhancing mitochondrial fatty acid β-oxidation; PKA inhibition nullifies these effects.\",\n      \"method\": \"Hepatocyte-specific TBC1D15 overexpression mouse model, co-immunoprecipitation, domain-mapping (10–180 aa), immunofluorescence microscopy, PKA inhibitor experiments, transmission electron microscopy\",\n      \"journal\": \"Metabolism: clinical and experimental\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — domain-mapped interaction with mechanistic pharmacological rescue, single lab\",\n      \"pmids\": [\"40334909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Tbc1d15 knockdown in vivo activates autophagy, reduces α-synuclein-mediated neurotoxicity, and improves motor performance in a mouse model of Parkinson's disease, consistent with TBC1D15 acting as an inhibitor of autophagic flux via Rab7 GAP activity.\",\n      \"method\": \"In vivo Tbc1d15 knockdown (mouse), autophagy flux assays, α-synuclein aggregate quantification, motor behavior testing\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 2–3 — in vivo KD with functional readout but preprint, single lab, no peer review\",\n      \"pmids\": [\"bio_10.1101_2024.10.01.616109\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"TBC1D15 is a multifunctional TBC-domain protein that acts primarily as a Rab7 GTPase-activating protein (GAP) to inactivate Rab7 and thereby control late endosome/lysosome morphology, mitophagy flux, and autophagic lysosomal reformation; it is recruited to the mitochondrial outer membrane by direct binding to Fis1, where it also interacts with Drp1 (via its C-terminal 574–624 domain) to drive asymmetrical mitochondrial fission, regulates mitochondria-lysosome contact duration, and in the nucleus-cytoplasm axis stabilizes oncoproteins such as NOTCH1 by blocking CDK8-mediated phosphodegron phosphorylation, while additionally functioning as a GAP for Arl4D and as a scaffold for lysosomal membrane regeneration downstream of ATG8 and LIMP2.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TBC1D15 is a Rab7 GTPase-activating protein and multifunctional scaffold that integrates late endosome/lysosome dynamics, mitochondrial fission, and autophagic membrane recycling. Its TBC domain catalyzes GTP hydrolysis on Rab7 (and Arl4D) via a conserved dual-finger mechanism, thereby controlling lysosomal size, GLUT4 trafficking through the late endosomal compartment, and autophagy flux [PMID:20363736, PMID:28168758, PMID:30316925, PMID:41709823]. TBC1D15 is recruited to the mitochondrial outer membrane by direct binding to Fis1 (through a conserved SKY-insert-dependent interface), where it further engages Drp1 via its C-terminal 574–624 domain to drive asymmetrical mitochondrial fission and regulate mitochondria–lysosome contact duration [PMID:23077178, PMID:35680100, PMID:37777154]. Following lysosomal damage, TBC1D15 is recruited via LIMP2–ATG8 and scaffolds the autophagic lysosomal reformation machinery (dynamin-2, kinesin-5B, clathrin) for membrane regeneration, and at the mitochondrial surface it stabilizes NOTCH1 by blocking CDK8-mediated phosphodegron phosphorylation [PMID:37024685, PMID:38409448].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Establishing that TBC1D15 is a selective Rab7 GAP answered the fundamental question of which TBC protein controls late endosome/lysosome identity, linking its activity to lysosomal morphology and cell survival.\",\n      \"evidence\": \"Effector pull-down (RILP–Rab7-GTP), lysosome imaging, selectivity controls against Rab4/5/11 in mammalian cells\",\n      \"pmids\": [\"20363736\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural basis for Rab7 selectivity at this stage\", \"Upstream regulators of TBC1D15 recruitment unknown\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identifying Fis1 as the mitochondrial receptor for TBC1D15 revealed how a cytosolic Rab-GAP is targeted to the mitochondrial outer membrane, establishing a previously unrecognized connection between endolysosomal Rab7 signaling and mitochondrial dynamics.\",\n      \"evidence\": \"Bacterially reconstituted direct Fis1–TBC1D15 complex, reciprocal co-IP from HeLa cells, fluorescence relocalization, siRNA knockdown morphology\",\n      \"pmids\": [\"23077178\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Binding interface on Fis1 not mapped at residue level\", \"Whether Rab7 GAP activity is required for the mitochondrial morphology phenotype untested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Work in Drosophila demonstrated that Rab7-GAP control of endolysosomal trafficking by TBC1D15 orthologs extends to synaptic growth, while mammalian studies revealed additional non-GAP functions including Numb/p53 complex disruption and RhoA cortical regulation.\",\n      \"evidence\": \"Drosophila loss-of-function/Rab7 epistasis at NMJ; mammalian AP-MS identifying Numb interaction; siRNA-mediated RhoA activation and membrane blebbing phenotype\",\n      \"pmids\": [\"23812537\", \"23468968\", \"24337944\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"RhoA regulation mechanism (direct or indirect) not resolved\", \"Numb interaction domain overlap with GAP domain not tested\", \"Synaptic overgrowth phenotype not confirmed in mammalian neurons\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Crystal structures of the TBC1D15 GAP domain combined with active-site mutagenesis established the dual-finger catalytic mechanism, while functional studies positioned TBC1D15 as a specific mediator coupling inflammasome signals to STING pathway suppression.\",\n      \"evidence\": \"X-ray crystallography (2.5–2.8 Å), Arg/Gln catalytic mutants; siRNA epistasis separating TBC1D15 from Drp1 in STING regulation\",\n      \"pmids\": [\"28168758\", \"28729291\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No Rab7-bound co-crystal structure\", \"STING pathway placement relies on knockdown epistasis without direct binding evidence\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"CRISPR knockout of TBC1D15 showed that its Rab7 GAP activity controls GLUT4 trafficking, with loss causing GLUT4 accumulation in Rab7-positive late endosomes and reduced glucose uptake.\",\n      \"evidence\": \"CRISPR/Cas9 KO, fluorescent glucose analog uptake, GLUT4–Rab7/LAMP1 co-localization\",\n      \"pmids\": [\"30316925\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Insulin-stimulated GLUT4 exocytosis not tested\", \"Rescue with GAP-dead mutant not performed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Placing Annexin A6 upstream of TBC1D15 as a stimulator of its Rab7-GAP activity linked TBC1D15 to cholesterol export pathways at late endosome–ER membrane contact sites, expanding its role beyond organelle morphology.\",\n      \"evidence\": \"Co-IP, Rab7-GTP effector pull-down, live imaging, EM of membrane contacts in NPC1 mutant cells\",\n      \"pmids\": [\"31664461\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct AnxA6–TBC1D15 binding not reconstituted in vitro\", \"Cholesterol flux measurements indirect\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Studies demonstrated that both the Fis1-binding and Rab7-GAP domains of TBC1D15 are independently required for regulating mitochondria–lysosome contacts and mitophagy flux, while a conserved miR-1–TBC1D15–Rab7 axis was shown to control autophagic clearance of α-synuclein.\",\n      \"evidence\": \"Domain-mutation rescue experiments with live imaging and cardiac functional assessment; miR-1 manipulation with cross-species genetic analysis (human to C. elegans)\",\n      \"pmids\": [\"33042281\", \"31958036\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of Fis1–TBC1D15 complex at contacts not determined\", \"miR-1 regulation in non-neuronal contexts not characterized\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identification of the C-terminal 574–624 domain as the Drp1-binding interface resolved how TBC1D15 drives asymmetrical mitochondrial fission at mitochondria–lysosome contact sites, distinguishing this function from its Rab7-GAP and Fis1-binding activities.\",\n      \"evidence\": \"Cardiac-specific knockin/knockout mice, domain-deletion/point-mutant rescue, time-lapse confocal microscopy, co-IP\",\n      \"pmids\": [\"35680100\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct structural basis of TBC1D15–Drp1 interaction not resolved\", \"Whether asymmetric fission occurs in non-cardiac tissues untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Discovery that LIMP2–ATG8 recruits TBC1D15 to damaged lysosomes for autophagic lysosomal reformation recast TBC1D15 as a scaffolding platform for membrane regeneration machinery (dynamin-2, kinesin-5B, clathrin), while parallel work mapped the Fis1 SKY-insert as the determinant of productive TBC1D15/DRP1 mitochondrial recruitment.\",\n      \"evidence\": \"Proximity-labeling proteomics, reciprocal co-IPs, live imaging of lysosomal tubulation; structure-guided FIS1 mutagenesis with YFP-TBC1D15 recruitment assay\",\n      \"pmids\": [\"37024685\", \"37777154\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Order of scaffold assembly (dynamin-2 vs. kinesin-5B recruitment) not resolved\", \"Whether ALR scaffolding requires TBC1D15 GAP activity is untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Expanding its substrate repertoire, TBC1D15 was shown to function as a GAP for Arl4D, regulating Arl4D mitochondrial translocation, while mechanistic work demonstrated that TBC1D15 stabilizes NOTCH1 by blocking CDK8-mediated phosphodegron phosphorylation and interacts with DNA-PKcs to promote its cytosolic retention.\",\n      \"evidence\": \"In vitro Arl4D GAP assay with domain mapping; CDK8 kinase assays and triple-KO hepatocyte mouse model for NOTCH1; LC-MS/MS identification and domain-deletion for DNA-PKcs interaction\",\n      \"pmids\": [\"41709823\", \"38409448\", \"38045047\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Arl4D GAP activity not independently confirmed\", \"Whether NOTCH1 stabilization requires Rab7 GAP activity unknown\", \"DNA-PKcs cytosolic retention mechanism not structurally characterized\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"TBC1D15 was found to recruit PLIN5 to mitochondria via its N-terminal 10–180 domain, promoting mitochondria–lipid droplet contacts and PKA-dependent PLIN5 nuclear translocation that upregulates fatty acid β-oxidation genes, revealing a new organelle contact function.\",\n      \"evidence\": \"Hepatocyte-specific TBC1D15 overexpression mouse model, co-IP, domain-mapping, PKA inhibitor experiments, TEM\",\n      \"pmids\": [\"40334909\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct TBC1D15–PLIN5 binding not reconstituted with purified proteins\", \"Whether ethanol-induced mitochondrial translocation of TBC1D15 requires Fis1 not tested\", \"Relationship to TBC1D15's Rab7 GAP activity in this context unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include how TBC1D15's multiple binding interfaces (Fis1, Drp1, ATG8, PLIN5, DNA-PKcs, NOTCH1) are coordinated or compete, whether its GAP activity toward Rab7 versus Arl4D is differentially regulated, and the structural basis of its scaffold functions in ALR and mitochondrial fission.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No full-length TBC1D15 structure available\", \"Competition or cooperativity among binding partners not systematically tested\", \"Tissue-specific regulation of TBC1D15 functions poorly understood\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [1, 2, 14]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2, 5, 6, 14]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [9, 15, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 6, 8, 16, 17]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [1, 6, 9]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [5, 13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [7, 9]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 6, 8, 9]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 5, 13]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [15]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [17]}\n    ],\n    \"complexes\": [\n      \"Fis1-TBC1D15-Drp1 mitochondrial fission complex\",\n      \"LIMP2-ATG8-TBC1D15 ALR scaffold\"\n    ],\n    \"partners\": [\n      \"FIS1\",\n      \"RAB7A\",\n      \"DRP1\",\n      \"LIMP2\",\n      \"ANXA6\",\n      \"PLIN5\",\n      \"ARL4D\",\n      \"NOTCH1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}