{"gene":"DEPDC5","run_date":"2026-04-28T17:46:02","timeline":{"discoveries":[{"year":2013,"finding":"DEPDC5 was identified as a component of the GATOR1 complex that functions as a repressor/negative regulator of the mTORC1 signaling pathway, specifically the amino acid-sensing branch; loss-of-function mutations cause hyperactivation of mTORC1.","method":"Exome sequencing identifying mutations; functional inference from shared homology and pathway context; subsequent in vitro TORC1 signaling assays","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 2 — independently replicated in two simultaneous Nature Genetics papers and confirmed by multiple subsequent functional studies","pmids":["23542697","23542701"],"is_preprint":false},{"year":2014,"finding":"DEPDC5 variants disrupt GATOR1 complex formation and/or DEPDC5-dependent inhibition of TORC1 signaling, as assessed by functional assays of 10 epilepsy-associated variants and 2 ovarian tumor variants; three variants clearly disrupted mTORC1 inhibition.","method":"In vitro TORC1 signaling assays and GATOR1 complex formation assays on epilepsy-associated DEPDC5 variants","journal":"Human mutation","confidence":"High","confidence_rationale":"Tier 1 — direct in vitro functional assay with multiple variants and mutagenesis approach","pmids":["25366275"],"is_preprint":false},{"year":2015,"finding":"DEPDC5 loss-of-function mutations lead to mTORC1 pathway activation (evidenced by mTOR activation marker immunostaining in resected brain tissue from patients with focal cortical dysplasia), establishing DEPDC5 as a negative regulator of mTOR in human brain tissue.","method":"Immunostaining of resected brain tissue for mTOR activation markers; germline and somatic sequencing","journal":"Annals of clinical and translational neurology","confidence":"Medium","confidence_rationale":"Tier 2 — direct tissue immunostaining in human specimens with genetic confirmation, single lab","pmids":["26000329"],"is_preprint":false},{"year":2016,"finding":"Homozygous Depdc5 knockout in rats causes embryonic lethality with constitutive mTORC1 hyperactivation (enhanced phosphorylation of S6K1 and rpS6) in brain and cultured fibroblasts; rapamycin treatment rescues the embryonic lethal phenotype, confirming DEPDC5 acts upstream of mTORC1.","method":"TALEN-generated global Depdc5 knockout rat; phosphorylation assays for mTORC1 effectors; prenatal rapamycin rescue experiment","journal":"Neurobiology of disease","confidence":"High","confidence_rationale":"Tier 1 — in vivo knockout with mechanistic rescue by mTORC1 inhibitor, multiple orthogonal readouts","pmids":["26873552"],"is_preprint":false},{"year":2017,"finding":"Neuron-specific Depdc5 conditional knockout mice (Syn1-Cre) develop mTORC1 hyperactivation exclusively in neurons (increased pS6), dysplastic and ectopic neurons, reactive astrogliosis, and seizures; mTORC1 hyperactivation is not observed in astrocytes despite reactive gliosis.","method":"Cre-lox conditional knockout mouse; immunohistochemistry for pS6; EEG; chemoconvulsant seizure threshold assay","journal":"Neurobiology of disease","confidence":"High","confidence_rationale":"Tier 2 — clean conditional KO with multiple orthogonal phenotypic readouts and cell-type specificity established","pmids":["29274432"],"is_preprint":false},{"year":2017,"finding":"DEPDC5 knockout in mice causes severe embryonic dysmorphology with mTORC1 hyperactivity observable in brain and in fibroblasts and neurospheres from knockout embryos cultured in nutrient-deprived conditions, confirming DEPDC5 role in nutrient-sensing mTORC1 regulation.","method":"CRISPR-generated null mouse; phosphorylation assays in primary fibroblasts and neurospheres under nutrient deprivation","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 — in vivo knockout plus in vitro nutrient-deprivation mechanistic assay, replicated across cell types","pmids":["28974734"],"is_preprint":false},{"year":2018,"finding":"Biallelic (germline + brain somatic second-hit) DEPDC5 inactivation causes focal cortical dysplasia with a mutation gradient—higher mosaicism in the seizure-onset zone; CRISPR-Cas9/in utero electroporation mosaic Depdc5 inactivation in mice recapitulates focal epilepsy with FCD and SUDEP-like events; Depdc5 loss shapes dendrite and spine morphology of excitatory neurons.","method":"Deep sequencing of postoperative human tissue; CRISPR-Cas9 with in utero electroporation mouse model; neuromorphological analysis","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1–2 — human tissue molecular evidence combined with in vivo CRISPR mouse model with multiple orthogonal readouts","pmids":["29708508"],"is_preprint":false},{"year":2018,"finding":"Depdc5 knockdown in neural progenitor cells and neurons causes mTORC1 (but not mTORC2) hyperactivation, increased soma size, increased filopodial extension, and inappropriate lysosomal localization of mTOR during amino acid starvation; these effects are reversed by rapamycin.","method":"shRNA knockdown in mouse neuroblastoma (N2aC) and mouse neural progenitor cells; immunofluorescence for lysosomal mTOR localization; rapamycin rescue","journal":"Neurobiology of disease","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal readouts in two neuronal cell types with pharmacological rescue","pmids":["29481864"],"is_preprint":false},{"year":2018,"finding":"Depdc5 knockdown in zebrafish leads to motor hyperactivity and increased neuronal activity dependent on mTORC1; rescue by wild-type DEPDC5 but not by epilepsy-associated mutants (p.Arg487* and p.Arg485Gln), confirming these are loss-of-function alleles.","method":"Morpholino-based zebrafish knockdown model; behavioral assays; overexpression of WT vs. mutant DEPDC5; rapamycin treatment","journal":"Annals of clinical and translational neurology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal rescue experiments with WT vs. mutant constructs and pharmacological inhibitor in vertebrate model","pmids":["29761115"],"is_preprint":false},{"year":2018,"finding":"Somatic focal Depdc5 deletion (via in utero electroporation with CRISPR) in rat embryonic brain produces spontaneous seizures with electroclinical features of focal cortical dysplasia type IIA, establishing that focal loss of DEPDC5 is sufficient to generate FCD-like epilepsy.","method":"In utero electroporation + CRISPR-based somatic Depdc5 deletion in rat; EEG recording; histopathology","journal":"Annals of neurology","confidence":"High","confidence_rationale":"Tier 1–2 — direct in vivo CRISPR somatic deletion with EEG and histological confirmation","pmids":["30080265"],"is_preprint":false},{"year":2018,"finding":"DEPDC5 inhibits the AKT-mTORC1-S6 axis through RagA (distinct from TSC1, which acts via Rheb); knockout of DEPDC5 in T-cell and monocyte cell lines enhances HIV-1 reactivation reversible by rapamycin, placing DEPDC5 as a negative regulator of mTORC1 via the RagA GTPase.","method":"Genome-wide CRISPR screen; gene knockout in cell lines; rapamycin rescue; mechanistic dissection of TSC1 vs. DEPDC5 pathways","journal":"Emerging microbes & infections","confidence":"Medium","confidence_rationale":"Tier 2 — CRISPR screen with mechanistic follow-up in two cell lines, single lab","pmids":["30087333"],"is_preprint":false},{"year":2019,"finding":"DEPDC5, as a component of GATOR1, is phosphorylated by Pim1 and AKT kinases at consensus sequences; this phosphorylation releases GATOR1-mediated inhibition of mTORC1. Phospho-inactive DEPDC5 mutants and DEPDC5 knockout partially block the ability of Pim/AKT inhibitors to suppress tumor growth and mTORC1 activity; knock-in of phospho-mimic S1530E confers resistance to Pim and AKT inhibitors.","method":"Phospho-specific antibodies; phospho-inactive mutant transfection; DEPDC5 knockout; phospho-mimic knock-in in tumor cells; in vitro and in vivo tumor growth assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — phosphorylation confirmed by antibodies and mutagenesis, functional consequence validated in vitro and in vivo","pmids":["31548394"],"is_preprint":false},{"year":2019,"finding":"Depdc5 loss in neurons leads to mTORC1-dependent reduction in levels of the other GATOR1 subunits NPRL2 and NPRL3; rapamycin rescues mTORC1 hyperactivation (pS6) but not GATOR1 protein levels, indicating a downstream effect on complex stability.","method":"Western blotting of GATOR1 subunits in Depdc5cc+ knockout mouse brain; rapamycin treatment","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 — clean KO with orthogonal protein level measurements and pharmacological rescue, single lab","pmids":["31174205"],"is_preprint":false},{"year":2019,"finding":"DEPDC5 inactivation in GIST (gastrointestinal stromal tumor) cells reduces cell proliferation through the mTORC1 signaling pathway, induces cell-cycle arrest, and promotes tumor growth in vitro and in vivo; DEPDC5 is validated as a tumor suppressor.","method":"Whole-exome sequencing of GISTs; DEPDC5 inactivation in cell lines; DEPDC5 overexpression in vitro; nude mouse xenograft assay; mTORC1 pathway analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal functional assays (KO, OE, in vivo xenograft) with mTORC1 pathway mechanistic readouts","pmids":["31636198"],"is_preprint":false},{"year":2019,"finding":"Second-hit DEPDC5 somatic mutations are restricted to dysmorphic neurons in focal cortical dysplasia IIA, and the somatic mutation load correlates with dysmorphic neuron density and the epileptogenic zone, confirming cell-autonomous mTORC1 hyperactivation drives the dysplastic phenotype.","method":"Deep sequencing of laser-captured dysmorphic neurons from human surgical tissue; correlation analysis","journal":"Annals of clinical and translational neurology","confidence":"High","confidence_rationale":"Tier 2 — cell-type-specific deep sequencing with functional correlation in human tissue","pmids":["31353856"],"is_preprint":false},{"year":2020,"finding":"Acute Depdc5 knockdown (~40–80%) in primary cortical neurons causes mTOR hyperactivation, increased soma size, dendritic arborization, increased excitatory synaptic transmission (mEPSC frequency and amplitude), increased density of excitatory synapses, and glutamate receptor expression, while inhibitory synapses are unaffected—demonstrating an excitation/inhibition imbalance causally linked to Depdc5 loss.","method":"RNAi-mediated acute Depdc5 knockdown in primary cortical cultures; electrophysiology (mEPSC/mIPSC recording); immunocytochemistry for synaptic markers","journal":"Neurobiology of disease","confidence":"High","confidence_rationale":"Tier 1–2 — electrophysiology combined with morphological and molecular assays, dose-dependent effect established","pmids":["32113911"],"is_preprint":false},{"year":2020,"finding":"Depdc5 knockout (but not Tsc2 knockout) cells fail to reduce mTOR lysosomal localization or S6/4E-BP1 phosphorylation in amino acid-free conditions, demonstrating that DEPDC5 specifically mediates amino acid-sensing-dependent lysosomal recruitment/inactivation of mTOR in neurons.","method":"CRISPR-edited Neuro2a cells and differentiated neurons; CFP/YFP FRET-biosensor for 4E-BP1 phosphorylation; confocal imaging of mTOR lysosomal localization during amino acid starvation","journal":"Experimental neurology","confidence":"High","confidence_rationale":"Tier 1 — live-cell FRET biosensor plus confocal imaging with mechanistic comparison of Depdc5 vs Tsc2 KO","pmids":["32781001"],"is_preprint":false},{"year":2021,"finding":"Depdc5 deficiency in hepatocytes leads to mTORC1 hyperactivation and suppression of PPARα pathway, causing exacerbation of alcohol-induced hepatic steatosis; the steatotic phenotype is reversed by the mTORC1 inhibitor Torin1 or by fenofibrate (PPARα agonist), placing DEPDC5 upstream of mTORC1–PPARα axis in hepatocytes.","method":"Hepatocyte-specific Depdc5 conditional knockout mouse (Depdc5-LKO); ethanol feeding model; Torin1 and fenofibrate pharmacological rescue; liver histology and lipid measurements","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 1–2 — clean conditional KO with pharmacological rescue identifying the downstream PPARα pathway","pmids":["34267188"],"is_preprint":false},{"year":2022,"finding":"Brain mTORC1 signaling is reduced after acute fasting in mice; DEPDC5 (GATOR1 component) is required for neuronal mTORC1 to sense amino acid withdrawal (leucine, arginine, glutamine); neuronal Depdc5 knockout mice are resistant to amino acid fluctuations after fasting and to the seizure-protective effects of fasting, establishing DEPDC5 as the essential link between amino acid sensing and mTORC1 regulation in neurons mediating fasting-induced seizure protection.","method":"Neuronal Depdc5 conditional knockout mice; metabolomics; seizure threshold assays after fasting; leucine/arginine/glutamine deprivation assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1–2 — clean conditional KO with metabolomics and in vivo seizure readout, multiple orthogonal methods","pmids":["36044864"],"is_preprint":false},{"year":2023,"finding":"Depdc5 deletion in excitatory neurons (cortical layer 5 and dentate gyrus) but not in cortical interneurons is sufficient to cause frequent generalized tonic-clonic seizures and SUDEP-like events; ictal apnea occurs before terminal cardiac asystole, and baseline respiratory dysfunction precedes SUDEP, implicating excitatory neuron-mediated respiratory dysregulation in SUDEP.","method":"Cell-type-specific Cre-lox Depdc5 knockout mice; EEG; simultaneous EEG-ECG; respiratory recordings; hypoxia challenge","journal":"Annals of neurology","confidence":"High","confidence_rationale":"Tier 2 — multiple cell-type-specific KO lines with simultaneous multimodal physiological recordings","pmids":["37606181"],"is_preprint":false},{"year":2024,"finding":"DEPDC5 interacts with USP46 (ubiquitin-specific protease 46), WDR48, and WDR20 as binding partners; loss of DEPDC5 leads to mTORC1-dependent USP46 upregulation, decreased GluA1 ubiquitination, and increased surface GluA1-containing AMPA receptors—shifting glutamate quantal size upward and increasing excitatory synaptic strength. USP46 knockdown or rapamycin rescues this phenotype.","method":"Co-immunoprecipitation/protein interaction network analysis; Depdc5 conditional knockout mouse; electrophysiology (quantal size); ubiquitination assay; USP46 knockdown rescue; rapamycin rescue","journal":"Neurobiology of disease","confidence":"High","confidence_rationale":"Tier 1–2 — interaction identified by Co-IP, mechanistic pathway established through KO + rescue with both genetic (USP46 KD) and pharmacological (rapamycin) approaches and electrophysiological readout","pmids":["40467011"],"is_preprint":false},{"year":2024,"finding":"In T cell-specific Depdc5 knockout mice, DEPDC5-deficient CD8+ T cells produce high levels of xanthine oxidase and lipid ROS due to hyper-mTORC1-induced ATF4 expression, leading to spontaneous ferroptosis and reduced peripheral CD8+ T cell numbers.","method":"T cell-specific Depdc5 conditional knockout mice; ROS measurement; xanthine oxidase assay; ATF4 expression analysis; ferroptosis markers","journal":"Cell discovery","confidence":"High","confidence_rationale":"Tier 2 — clean conditional KO with multiple orthogonal mechanistic readouts identifying the mTORC1-ATF4-xanthine oxidase-ferroptosis axis","pmids":["38763950"],"is_preprint":false},{"year":2024,"finding":"Biallelic inactivation of Depdc5 in mouse medial prefrontal cortex leads to shared alterations in pyramidal neuron morphology, positioning, and membrane excitability compared with other mTORC1 pathway gene knockouts, but causes gene-specific differences in excitatory synaptic transmission.","method":"In utero electroporation for biallelic inactivation; patch-clamp electrophysiology; morphological analysis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1–2 — direct in vivo manipulation with electrophysiology and morphological readouts, comparator design across multiple genes","pmids":["38411613"],"is_preprint":false},{"year":2018,"finding":"DEPDC5 down-regulation in hepatic stellate cells leads to increased β-catenin expression and production of MMP2 (matrix metallopeptidase 2), a secreted enzyme involved in fibrosis progression, identifying a DEPDC5–β-catenin–MMP2 pathway in hepatic stellate cells distinct from mTORC1.","method":"DEPDC5 siRNA knockdown in immortalized hepatic stellate cells (LX-2); β-catenin and MMP2 expression assays","journal":"Hepatology (Baltimore, Md.)","confidence":"Medium","confidence_rationale":"Tier 3 — single in vitro knockdown experiment, single lab, no rescue or mechanistic follow-up","pmids":["26517016"],"is_preprint":false},{"year":2018,"finding":"DEPDC5 knockout in hepatocellular carcinoma cells leads to resistance to leucine starvation via impaired autophagy (reduced LC3-II, p62 accumulation, and ROS tolerance); DEPDC5 overexpression suppresses cell proliferation and tumorigenicity in immunocompromised mice, and promotes p62 degradation with increased ROS susceptibility.","method":"CRISPR/Cas9 DEPDC5 knockout in HCC cells; LC3-II/p62 western blotting; ROS assay; xenograft mouse model","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — CRISPR KO and OE with in vitro and in vivo readouts, single lab","pmids":["29311600"],"is_preprint":false},{"year":2019,"finding":"Focal perineuronal net (PNN) degradation by proteolytic enzymes occurs in the malformed cortex of forebrain Depdc5-knockout mice prior to seizures, coincident with microglia inflammation, resulting in parvalbumin interneuron loss and impaired presynaptic inhibition.","method":"Forebrain-specific Depdc5 conditional knockout mouse; immunohistochemistry for PNNs (WFA staining), parvalbumin, and microglial markers; electrophysiology","journal":"Developmental neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 — conditional KO with immunohistochemical and electrophysiological readouts, single lab, non-cell-autonomous mechanism identified","pmids":["35580549"],"is_preprint":false},{"year":2024,"finding":"DEPDC5 protein degradation in colorectal cancer is mediated through chaperone-mediated autophagy (CMA) downstream of the GPR81/lactate signaling axis; SNX10 interacts with DEPDC5 and recruits it to lysosomes for CMA-mediated degradation, activating mTORC1 and promoting EMT and metastasis.","method":"siRNA knockdown; Co-IP demonstrating SNX10-DEPDC5 interaction; western blotting for CMA markers; in vivo lung metastasis mouse model","journal":"Phytomedicine : international journal of phytotherapy and phytopharmacology","confidence":"Medium","confidence_rationale":"Tier 3 — Co-IP showing interaction plus functional knockdown, in vivo model; single lab","pmids":["38615493"],"is_preprint":false},{"year":2025,"finding":"A DEPDC5 missense variant (p.Phe685Leu) causes altered subcellular localization of the mutant protein in primary neurons and, when knocked into mice (hDEPDC5F685L), produces mTOR hyperactivation, enlarged neuronal soma, abnormal neurons, and heightened seizure susceptibility; rapamycin rescues neuronal size and mTOR activity and reduces seizure susceptibility.","method":"Mutant plasmid transfection for localization; nervous system-specific knock-in mouse; immunohistochemistry; seizure threshold assays; rapamycin rescue","journal":"Neurobiology of disease","confidence":"High","confidence_rationale":"Tier 1–2 — knock-in mouse with localization data and pharmacological rescue, multiple readouts","pmids":["39954744"],"is_preprint":false},{"year":2025,"finding":"Postnatal focal cortical DEPDC5 loss (without disrupting embryonic cortical migration) is sufficient to cause mTOR hyperactivation, FCD pathological hallmarks (increased SMI-311 neurofilament, hypomyelination, astrogliosis, microglial activation), lowered seizure thresholds, increased focal seizures, and increased seizure-induced death, demonstrating a cell-autonomous postnatal role of DEPDC5.","method":"Postnatal AAV-Cre injection in floxed Depdc5 mice; histopathology; EEG; seizure threshold assays","journal":"JCI insight","confidence":"High","confidence_rationale":"Tier 2 — clean focal postnatal KO with multiple histopathological and electrophysiological readouts","pmids":["40996830"],"is_preprint":false},{"year":2026,"finding":"Mosaic biallelic DEPDC5 two-hit inactivation in human cortical organoids (hCOs) causes increased mTOR activity (rescued by rapamycin), dysmorphic-like neurons, enhanced neuronal excitability, premature upper-layer neuron generation, dysregulated Notch and Wnt signaling in neural progenitors, and altered metabolism and translation—establishing cell-autonomous effects of DEPDC5 biallelic loss during human corticogenesis.","method":"Patient-derived human cortical organoids with mosaic DEPDC5 two-hit deletion; single-cell transcriptomics; electrophysiology; rapamycin rescue; immunofluorescence","journal":"Brain : a journal of neurology","confidence":"High","confidence_rationale":"Tier 1–2 — human organoid model with single-cell transcriptomics, electrophysiology, and pharmacological rescue","pmids":["41789478"],"is_preprint":false}],"current_model":"DEPDC5 is a core subunit of the GATOR1 complex (together with NPRL2 and NPRL3) that functions as a GTPase-activating protein (GAP) toward RagA/B GTPases, acting as the primary amino acid–sensing brake on lysosomal mTORC1 recruitment and activation; loss of DEPDC5 causes constitutive mTORC1 hyperactivation that drives neuronal soma enlargement, dysplastic morphology, altered dendritic/synaptic structure, excitation–inhibition imbalance (via USP46-mediated GluA1 deubiquitination and AMPA receptor surface accumulation), and focal cortical dysplasia-associated epilepsy, while upstream Pim1/AKT kinases can phosphorylate DEPDC5 to release this inhibition, and DEPDC5 also controls CD8+ T cell ferroptosis via an mTORC1–ATF4–xanthine oxidase axis."},"narrative":{"teleology":[{"year":2013,"claim":"Identifying DEPDC5 as a GATOR1 subunit and mTORC1 repressor answered what molecular complex mediates amino acid–dependent mTORC1 inhibition and linked its loss-of-function to familial focal epilepsy.","evidence":"Exome sequencing in epilepsy families combined with functional mTORC1 signaling assays","pmids":["23542697","23542701"],"confidence":"High","gaps":["GAP activity toward Rag GTPases not yet directly demonstrated","structural basis of GATOR1 complex assembly unknown","mechanism linking mTORC1 hyperactivation to seizures uncharacterized"]},{"year":2014,"claim":"Systematic functional testing of epilepsy-associated DEPDC5 variants established that specific mutations disrupt GATOR1 complex integrity and/or mTORC1 inhibitory function, validating a loss-of-function mechanism for disease alleles.","evidence":"In vitro mTORC1 signaling and GATOR1 complex formation assays on 10 epilepsy-associated and 2 tumor-associated DEPDC5 variants","pmids":["25366275"],"confidence":"High","gaps":["structural basis of variant-specific disruption unknown","genotype–phenotype correlation for seizure severity not established"]},{"year":2016,"claim":"In vivo genetic ablation in rodents demonstrated that DEPDC5 is essential for embryonic viability and that constitutive mTORC1 hyperactivation is the causal downstream mechanism, as rapamycin rescued embryonic lethality.","evidence":"TALEN-generated Depdc5 knockout rat with mTORC1 phosphorylation assays and prenatal rapamycin rescue","pmids":["26873552"],"confidence":"High","gaps":["cell-type-specific requirements not yet dissected","whether mTORC1 is the sole effector of DEPDC5 loss not excluded"]},{"year":2017,"claim":"Neuron-specific conditional knockout resolved that DEPDC5 loss in neurons—not glia—drives mTORC1 hyperactivation, cortical dysplasia, and seizures, establishing cell-autonomous neuronal pathology.","evidence":"Syn1-Cre conditional Depdc5 knockout mouse with EEG, pS6 immunohistochemistry, and seizure threshold assays","pmids":["29274432","28974734"],"confidence":"High","gaps":["which neuronal subtypes are most vulnerable not determined","downstream effectors mediating seizure generation unknown"]},{"year":2018,"claim":"Demonstration that biallelic (germline + somatic second-hit) DEPDC5 inactivation is required for focal cortical dysplasia, and that focal somatic deletion alone recapitulates FCD and SUDEP in rodents, established the two-hit model and cell-autonomous sufficiency of DEPDC5 loss for epileptogenesis.","evidence":"Deep sequencing of human surgical tissue; CRISPR/in utero electroporation in mouse and rat; neuromorphological and EEG analysis","pmids":["29708508","30080265","31353856"],"confidence":"High","gaps":["timing of second-hit relative to cortical development not defined","whether migration defects are required for epileptogenesis unclear"]},{"year":2018,"claim":"Mechanistic dissection in neuronal cells showed DEPDC5 specifically controls amino acid–dependent lysosomal mTOR recruitment (distinct from TSC2/Rheb axis), explaining why DEPDC5 loss causes mTORC1 hyperactivation even during amino acid starvation.","evidence":"CRISPR Depdc5 vs Tsc2 knockout in Neuro2a cells; FRET biosensor for 4E-BP1 phosphorylation; confocal imaging of mTOR–lysosome colocalization","pmids":["32781001","29481864"],"confidence":"High","gaps":["direct GAP activity measurement on Rag GTPases in neuronal context not performed","whether nutrient-independent functions of DEPDC5 exist in neurons not addressed"]},{"year":2019,"claim":"Discovery that Pim1 and AKT phosphorylate DEPDC5 to release GATOR1-mediated mTORC1 inhibition established DEPDC5 as a signal-regulated node integrating growth factor and amino acid sensing, with direct therapeutic implications for kinase inhibitor resistance in cancer.","evidence":"Phospho-specific antibodies; phospho-inactive and phospho-mimic DEPDC5 mutants; DEPDC5 knockout tumor cells; in vivo xenograft assays","pmids":["31548394"],"confidence":"High","gaps":["phosphorylation sites not mapped at residue resolution beyond S1530","whether phosphorylation affects GATOR1 complex integrity or GAP activity not distinguished"]},{"year":2020,"claim":"Electrophysiological characterization revealed that DEPDC5 loss selectively increases excitatory but not inhibitory synaptic transmission, directly demonstrating that excitation–inhibition imbalance is a proximal mechanism of DEPDC5-associated epileptogenesis.","evidence":"Acute RNAi knockdown in primary cortical neurons; mEPSC/mIPSC recordings; synaptic marker immunocytochemistry","pmids":["32113911"],"confidence":"High","gaps":["molecular identity of upregulated glutamate receptors not fully characterized","contribution of presynaptic vs postsynaptic mechanisms not resolved"]},{"year":2022,"claim":"Establishing that neuronal DEPDC5 is required for mTORC1 to sense amino acid fluctuations during fasting—and that this sensing mediates fasting-induced seizure protection—linked DEPDC5's metabolic function to a clinically relevant anticonvulsant mechanism.","evidence":"Neuronal Depdc5 conditional knockout mice; metabolomics; seizure threshold assays after fasting; specific amino acid deprivation experiments","pmids":["36044864"],"confidence":"High","gaps":["which specific amino acid sensors upstream of GATOR1 are active in neurons not identified","whether dietary interventions can substitute for DEPDC5 function not tested"]},{"year":2023,"claim":"Cell-type-specific knockout showed that DEPDC5 loss in excitatory (but not inhibitory) neurons is sufficient for seizures and SUDEP, with ictal apnea preceding cardiac arrest, identifying respiratory circuit dysfunction as the proximal cause of SUDEP.","evidence":"Multiple Cre-driver Depdc5 knockout lines; simultaneous EEG-ECG-respiratory recordings; hypoxia challenge","pmids":["37606181"],"confidence":"High","gaps":["specific brainstem circuits mediating respiratory failure not identified","whether interventions targeting respiratory drive can prevent SUDEP not tested"]},{"year":2024,"claim":"Identification of USP46 as a DEPDC5-interacting deubiquitinase revealed the molecular mechanism by which DEPDC5 loss increases excitatory synaptic strength: mTORC1-dependent USP46 upregulation reduces GluA1 ubiquitination, increasing surface AMPA receptors and glutamate quantal size.","evidence":"Co-immunoprecipitation; Depdc5 conditional knockout; GluA1 ubiquitination assay; electrophysiology; USP46 knockdown and rapamycin rescue","pmids":["40467011"],"confidence":"High","gaps":["whether USP46 pathway is sufficient to explain all excitatory synaptic changes not established","reciprocal Co-IP for DEPDC5–USP46 not explicitly described"]},{"year":2024,"claim":"DEPDC5's role was extended beyond neurons: in CD8+ T cells, DEPDC5 loss causes hyper-mTORC1–driven ATF4 upregulation, xanthine oxidase production, lipid ROS accumulation, and spontaneous ferroptosis, establishing DEPDC5 as an immune cell survival factor.","evidence":"T cell–specific Depdc5 conditional knockout mice; ROS and xanthine oxidase assays; ATF4 expression; ferroptosis markers","pmids":["38763950"],"confidence":"High","gaps":["whether DEPDC5-dependent ferroptosis occurs in other immune cell types unknown","therapeutic relevance of modulating this axis in immunotherapy not tested"]},{"year":2025,"claim":"Postnatal focal DEPDC5 deletion demonstrated that cortical dysplasia and epilepsy can arise independently of embryonic migration defects, and a patient-derived missense knock-in confirmed that subcellular mislocalization of mutant DEPDC5 is sufficient for mTOR hyperactivation and seizure susceptibility.","evidence":"Postnatal AAV-Cre in floxed Depdc5 mice; knock-in mouse of hDEPDC5-F685L; rapamycin rescue; EEG and histopathology","pmids":["40996830","39954744"],"confidence":"High","gaps":["window of postnatal vulnerability not defined","structural basis of missense-induced mislocalization unknown"]},{"year":2026,"claim":"Human cortical organoids with mosaic biallelic DEPDC5 loss recapitulated dysmorphic neurons, hyperexcitability, and premature upper-layer neurogenesis with dysregulated Notch/Wnt signaling, establishing cell-autonomous human-specific developmental consequences of DEPDC5 loss.","evidence":"Patient-derived cortical organoids with mosaic two-hit DEPDC5 deletion; single-cell transcriptomics; electrophysiology; rapamycin rescue","pmids":["41789478"],"confidence":"High","gaps":["whether Notch/Wnt dysregulation is mTORC1-dependent or independent not resolved","organoid model lacks circuit-level validation"]},{"year":null,"claim":"Major open questions include the direct structural basis of DEPDC5's GAP activity toward Rag GTPases, identification of upstream amino acid sensors feeding into GATOR1 in neurons, whether non-mTORC1 functions of DEPDC5 contribute to disease, and whether targeting the USP46–GluA1 axis or ferroptosis pathway has therapeutic potential.","evidence":"","pmids":[],"confidence":"Medium","gaps":["no reconstituted GAP assay for human DEPDC5 on Rag GTPases","upstream amino acid sensors in neurons not identified","therapeutic window for postnatal intervention not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,3,10,11]},{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0,10,16]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[7,16,26]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[7,27]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,3,10,11,16,18]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[24]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[4,6,15,19,20,22]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[21]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[21]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[13,26]}],"complexes":["GATOR1"],"partners":["NPRL2","NPRL3","USP46","WDR48","WDR20","SNX10","RRAGA"],"other_free_text":[]},"mechanistic_narrative":"DEPDC5 is a core subunit of the GATOR1 complex that functions as the principal amino acid–sensing negative regulator of mTORC1, controlling lysosomal mTOR recruitment and activity via GTPase-activating protein function toward RagA/B GTPases. DEPDC5 loss abolishes mTORC1 suppression during amino acid withdrawal, causing constitutive mTORC1 hyperactivation that drives neuronal soma enlargement, dendritic dysmorphology, increased excitatory synaptic strength—including mTORC1-dependent USP46 upregulation leading to GluA1 deubiquitination and AMPA receptor surface accumulation—and excitation–inhibition imbalance [PMID:23542697, PMID:32781001, PMID:32113911, PMID:40467011]. Germline heterozygous DEPDC5 loss-of-function mutations combined with somatic second-hit inactivation cause focal cortical dysplasia and mTORC1-dependent epilepsy with SUDEP, where excitatory neuron loss drives respiratory dysregulation preceding terminal cardiac events [PMID:29708508, PMID:31353856, PMID:37606181]. Beyond neurons, DEPDC5 is phosphorylated by Pim1/AKT to release GATOR1-mediated mTORC1 inhibition in cancer cells, functions as a tumor suppressor in gastrointestinal stromal tumors, regulates hepatocyte PPARα-dependent lipid metabolism, and controls CD8+ T cell ferroptosis through an mTORC1–ATF4–xanthine oxidase axis [PMID:31548394, PMID:31636198, PMID:34267188, PMID:38763950]."},"prefetch_data":{"uniprot":{"accession":"O75140","full_name":"GATOR1 complex protein DEPDC5","aliases":["DEP domain-containing protein 5"],"length_aa":1603,"mass_kda":181.3,"function":"As a component of the GATOR1 complex functions as an inhibitor of the amino acid-sensing branch of the mTORC1 pathway (PubMed:23723238, PubMed:25457612, PubMed:29590090, PubMed:29769719, PubMed:31548394, PubMed:35338845). In response to amino acid depletion, the GATOR1 complex has GTPase activating protein (GAP) activity and strongly increases GTP hydrolysis by RagA/RRAGA (or RagB/RRAGB) within heterodimeric Rag complexes, thereby turning them into their inactive GDP-bound form, releasing mTORC1 from lysosomal surface and inhibiting mTORC1 signaling (PubMed:23723238, PubMed:25457612, PubMed:29590090, PubMed:29769719, PubMed:35338845). In the presence of abundant amino acids, the GATOR1 complex is negatively regulated by GATOR2, the other GATOR subcomplex, in this amino acid-sensing branch of the TORC1 pathway (PubMed:23723238, PubMed:25457612, PubMed:29769719). Within the GATOR1 complex, DEPDC5 mediates direct interaction with the nucleotide-binding pocket of small GTPases Rag (RagA/RRAGA, RagB/RRAGB, RagC/RRAGC and/or RagD/RRAGD) and coordinates their nucleotide loading states by promoting RagA/RRAGA or RagB/RRAGB into their GDP-binding state and RagC/RRAGC or RagD/RRAGD into their GTP-binding state (PubMed:29590090, PubMed:35338845). 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KLHL22","url":"https://www.omim.org/entry/618020"},{"mim_id":"617418","title":"WD REPEAT-CONTAINING PROTEIN 59; WDR59","url":"https://www.omim.org/entry/617418"},{"mim_id":"616512","title":"RING FINGER PROTEIN 152; RNF152","url":"https://www.omim.org/entry/616512"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in 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Folia pharmacologica Japonica","url":"https://pubmed.ncbi.nlm.nih.gov/30531098","citation_count":2,"is_preprint":false},{"pmid":"36733671","id":"PMC_36733671","title":"Correlation of DEPDC5 rs1012068 and rs5998152 Polymorphisms with Risk of Hepatocellular Carcinoma: A Systematic Review and Meta-Analysis.","date":"2023","source":"Journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36733671","citation_count":1,"is_preprint":false},{"pmid":"38983576","id":"PMC_38983576","title":"Nonsense mutation in DEPDC5 gene in a patient with carbamazepine-responsive focal epilepsy.","date":"2024","source":"Epilepsy & behavior reports","url":"https://pubmed.ncbi.nlm.nih.gov/38983576","citation_count":1,"is_preprint":false},{"pmid":"36639812","id":"PMC_36639812","title":"Neurophysiological assessment of cortical activity in DEPDC5- and NPRL3-related epileptic mTORopathies.","date":"2023","source":"Orphanet journal of rare diseases","url":"https://pubmed.ncbi.nlm.nih.gov/36639812","citation_count":1,"is_preprint":false},{"pmid":"41487148","id":"PMC_41487148","title":"α-hederin decreases the glycolysis level in intestinal epithelial cells via SNX10-mediated DEPDC5 degradation.","date":"2025","source":"Journal of pharmaceutical analysis","url":"https://pubmed.ncbi.nlm.nih.gov/41487148","citation_count":1,"is_preprint":false},{"pmid":"29588938","id":"PMC_29588938","title":"Partial deletion of DEPDC5 in a child with focal epilepsy.","date":"2016","source":"Epilepsia open","url":"https://pubmed.ncbi.nlm.nih.gov/29588938","citation_count":1,"is_preprint":false},{"pmid":"40188669","id":"PMC_40188669","title":"Explosive onset focal epilepsies without cortical malformation: A review of a pediatric cohort with pathogenic variations in the GATOR1 complex (DEPDC5, NPRL3 and NPRL2).","date":"2025","source":"Seizure","url":"https://pubmed.ncbi.nlm.nih.gov/40188669","citation_count":1,"is_preprint":false},{"pmid":"35907814","id":"PMC_35907814","title":"What is the impact of a novel DEPDC5 variant on an infant with focal epilepsy: a case report.","date":"2022","source":"BMC pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/35907814","citation_count":1,"is_preprint":false},{"pmid":"40100487","id":"PMC_40100487","title":"Genotypic and clinical phenotypic analysis of DEPDC5 gene mutations.","date":"2025","source":"Neurogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/40100487","citation_count":0,"is_preprint":false},{"pmid":"40543030","id":"PMC_40543030","title":"Splicing variants in DEPDC5-related epilepsies: From functional characterization to correction.","date":"2025","source":"Epilepsia","url":"https://pubmed.ncbi.nlm.nih.gov/40543030","citation_count":0,"is_preprint":false},{"pmid":"40996830","id":"PMC_40996830","title":"Focal DEPDC5 loss without disruption to cerebral cortical neuron migration recapitulates DEPDC5-related focal epilepsy.","date":"2025","source":"JCI insight","url":"https://pubmed.ncbi.nlm.nih.gov/40996830","citation_count":0,"is_preprint":false},{"pmid":"41427333","id":"PMC_41427333","title":"Early death and neuronal abnormalities in depdc5 loss-of-function mosaic zebrafish models.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41427333","citation_count":0,"is_preprint":false},{"pmid":"41789478","id":"PMC_41789478","title":"Mosaic human cortical organoids model mTOR-related focal cortical dysplasia through DEPDC5 deletion.","date":"2026","source":"Brain : a journal of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/41789478","citation_count":0,"is_preprint":false},{"pmid":"40467011","id":"PMC_40467011","title":"DEPDC5 regulates the strength of excitatory synaptic transmission by interacting with ubiquitin-specific protease 46.","date":"2025","source":"Neurobiology of disease","url":"https://pubmed.ncbi.nlm.nih.gov/40467011","citation_count":0,"is_preprint":false},{"pmid":"37722146","id":"PMC_37722146","title":"Generation of a human iPSC line CIPi003-A from a patient with focal epilepsy harboring a heterozygous mutation in DEPDC5 gene.","date":"2023","source":"Stem cell research","url":"https://pubmed.ncbi.nlm.nih.gov/37722146","citation_count":0,"is_preprint":false},{"pmid":"40742146","id":"PMC_40742146","title":"Identification of a Second-Hit Brain Somatic DEPDC5 Variant Supports Causality of a DEPDC5 Germline Variant of Uncertain Significance. Time for a Classification Update?","date":"2025","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/40742146","citation_count":0,"is_preprint":false},{"pmid":"41587632","id":"PMC_41587632","title":"Ectopically overexpressed glycine transporter 2 contributes to epileptogenesis in DEPDC5-related epilepsy.","date":"2026","source":"Experimental neurology","url":"https://pubmed.ncbi.nlm.nih.gov/41587632","citation_count":0,"is_preprint":false},{"pmid":"41954126","id":"PMC_41954126","title":"Cardiac remodeling and arrhythmia in a mouse model of Depdc5 haploinsufficiency.","date":"2026","source":"Epilepsia","url":"https://pubmed.ncbi.nlm.nih.gov/41954126","citation_count":0,"is_preprint":false},{"pmid":"40206130","id":"PMC_40206130","title":"Dual Diagnosis of Fragile X Syndrome and DEPDC5-Related Disorder Emphasizes DEPDC5's Role Beyond Familial Epilepsy: A Case Report and Literature Review.","date":"2025","source":"Case reports in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40206130","citation_count":0,"is_preprint":false},{"pmid":"40546503","id":"PMC_40546503","title":"DEPDC5-Related Familial Focal Epilepsy With Variable Foci-1: A Report of a Rare Case.","date":"2025","source":"Cureus","url":"https://pubmed.ncbi.nlm.nih.gov/40546503","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.27.678943","title":"Protein Biomarker in Focal Cortical Dysplasia: Molecular Clues to Pathogenesis","date":"2025-09-28","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.27.678943","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.25.661323","title":"Mosaic human cortical organoids model mTOR-related focal cortical dysplasia through DEPDC5 loss-of-function","date":"2025-06-25","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.25.661323","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.12.25.24319647","title":"Insights into<i>DEPDC5</i>-Related Epilepsy from 586 people: Variant Penetrance, Phenotypic Spectrum, and Treatment Outcomes","date":"2024-12-31","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.25.24319647","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.03.03.25321546","title":"Genomic Modifiers of Neurological Resilience in a Niemann-Pick C family","date":"2025-03-06","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.03.25321546","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.01.07.25320161","title":"Harnessing Mondo and the ILAE Classification for Curation and Analysis of 71,942 epilepsy patient variants","date":"2025-01-08","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.07.25320161","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.11.17.25340194","title":"Deep tissue sequencing improves genetic diagnostic yield in focal cortical dysplasia","date":"2025-11-22","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.17.25340194","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.06.11.24308522","title":"Exome Sequencing of 963 Chinese Families Identifies Novel Epilepsy Candidate Genes","date":"2024-06-11","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.11.24308522","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":44937,"output_tokens":7339,"usd":0.122448},"stage2":{"model":"claude-opus-4-6","input_tokens":11099,"output_tokens":3780,"usd":0.224993},"total_usd":0.347441,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"DEPDC5 was identified as a component of the GATOR1 complex that functions as a repressor/negative regulator of the mTORC1 signaling pathway, specifically the amino acid-sensing branch; loss-of-function mutations cause hyperactivation of mTORC1.\",\n      \"method\": \"Exome sequencing identifying mutations; functional inference from shared homology and pathway context; subsequent in vitro TORC1 signaling assays\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — independently replicated in two simultaneous Nature Genetics papers and confirmed by multiple subsequent functional studies\",\n      \"pmids\": [\"23542697\", \"23542701\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"DEPDC5 variants disrupt GATOR1 complex formation and/or DEPDC5-dependent inhibition of TORC1 signaling, as assessed by functional assays of 10 epilepsy-associated variants and 2 ovarian tumor variants; three variants clearly disrupted mTORC1 inhibition.\",\n      \"method\": \"In vitro TORC1 signaling assays and GATOR1 complex formation assays on epilepsy-associated DEPDC5 variants\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro functional assay with multiple variants and mutagenesis approach\",\n      \"pmids\": [\"25366275\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"DEPDC5 loss-of-function mutations lead to mTORC1 pathway activation (evidenced by mTOR activation marker immunostaining in resected brain tissue from patients with focal cortical dysplasia), establishing DEPDC5 as a negative regulator of mTOR in human brain tissue.\",\n      \"method\": \"Immunostaining of resected brain tissue for mTOR activation markers; germline and somatic sequencing\",\n      \"journal\": \"Annals of clinical and translational neurology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct tissue immunostaining in human specimens with genetic confirmation, single lab\",\n      \"pmids\": [\"26000329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Homozygous Depdc5 knockout in rats causes embryonic lethality with constitutive mTORC1 hyperactivation (enhanced phosphorylation of S6K1 and rpS6) in brain and cultured fibroblasts; rapamycin treatment rescues the embryonic lethal phenotype, confirming DEPDC5 acts upstream of mTORC1.\",\n      \"method\": \"TALEN-generated global Depdc5 knockout rat; phosphorylation assays for mTORC1 effectors; prenatal rapamycin rescue experiment\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vivo knockout with mechanistic rescue by mTORC1 inhibitor, multiple orthogonal readouts\",\n      \"pmids\": [\"26873552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Neuron-specific Depdc5 conditional knockout mice (Syn1-Cre) develop mTORC1 hyperactivation exclusively in neurons (increased pS6), dysplastic and ectopic neurons, reactive astrogliosis, and seizures; mTORC1 hyperactivation is not observed in astrocytes despite reactive gliosis.\",\n      \"method\": \"Cre-lox conditional knockout mouse; immunohistochemistry for pS6; EEG; chemoconvulsant seizure threshold assay\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean conditional KO with multiple orthogonal phenotypic readouts and cell-type specificity established\",\n      \"pmids\": [\"29274432\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"DEPDC5 knockout in mice causes severe embryonic dysmorphology with mTORC1 hyperactivity observable in brain and in fibroblasts and neurospheres from knockout embryos cultured in nutrient-deprived conditions, confirming DEPDC5 role in nutrient-sensing mTORC1 regulation.\",\n      \"method\": \"CRISPR-generated null mouse; phosphorylation assays in primary fibroblasts and neurospheres under nutrient deprivation\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vivo knockout plus in vitro nutrient-deprivation mechanistic assay, replicated across cell types\",\n      \"pmids\": [\"28974734\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Biallelic (germline + brain somatic second-hit) DEPDC5 inactivation causes focal cortical dysplasia with a mutation gradient—higher mosaicism in the seizure-onset zone; CRISPR-Cas9/in utero electroporation mosaic Depdc5 inactivation in mice recapitulates focal epilepsy with FCD and SUDEP-like events; Depdc5 loss shapes dendrite and spine morphology of excitatory neurons.\",\n      \"method\": \"Deep sequencing of postoperative human tissue; CRISPR-Cas9 with in utero electroporation mouse model; neuromorphological analysis\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — human tissue molecular evidence combined with in vivo CRISPR mouse model with multiple orthogonal readouts\",\n      \"pmids\": [\"29708508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Depdc5 knockdown in neural progenitor cells and neurons causes mTORC1 (but not mTORC2) hyperactivation, increased soma size, increased filopodial extension, and inappropriate lysosomal localization of mTOR during amino acid starvation; these effects are reversed by rapamycin.\",\n      \"method\": \"shRNA knockdown in mouse neuroblastoma (N2aC) and mouse neural progenitor cells; immunofluorescence for lysosomal mTOR localization; rapamycin rescue\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal readouts in two neuronal cell types with pharmacological rescue\",\n      \"pmids\": [\"29481864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Depdc5 knockdown in zebrafish leads to motor hyperactivity and increased neuronal activity dependent on mTORC1; rescue by wild-type DEPDC5 but not by epilepsy-associated mutants (p.Arg487* and p.Arg485Gln), confirming these are loss-of-function alleles.\",\n      \"method\": \"Morpholino-based zebrafish knockdown model; behavioral assays; overexpression of WT vs. mutant DEPDC5; rapamycin treatment\",\n      \"journal\": \"Annals of clinical and translational neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal rescue experiments with WT vs. mutant constructs and pharmacological inhibitor in vertebrate model\",\n      \"pmids\": [\"29761115\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Somatic focal Depdc5 deletion (via in utero electroporation with CRISPR) in rat embryonic brain produces spontaneous seizures with electroclinical features of focal cortical dysplasia type IIA, establishing that focal loss of DEPDC5 is sufficient to generate FCD-like epilepsy.\",\n      \"method\": \"In utero electroporation + CRISPR-based somatic Depdc5 deletion in rat; EEG recording; histopathology\",\n      \"journal\": \"Annals of neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct in vivo CRISPR somatic deletion with EEG and histological confirmation\",\n      \"pmids\": [\"30080265\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DEPDC5 inhibits the AKT-mTORC1-S6 axis through RagA (distinct from TSC1, which acts via Rheb); knockout of DEPDC5 in T-cell and monocyte cell lines enhances HIV-1 reactivation reversible by rapamycin, placing DEPDC5 as a negative regulator of mTORC1 via the RagA GTPase.\",\n      \"method\": \"Genome-wide CRISPR screen; gene knockout in cell lines; rapamycin rescue; mechanistic dissection of TSC1 vs. DEPDC5 pathways\",\n      \"journal\": \"Emerging microbes & infections\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — CRISPR screen with mechanistic follow-up in two cell lines, single lab\",\n      \"pmids\": [\"30087333\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"DEPDC5, as a component of GATOR1, is phosphorylated by Pim1 and AKT kinases at consensus sequences; this phosphorylation releases GATOR1-mediated inhibition of mTORC1. Phospho-inactive DEPDC5 mutants and DEPDC5 knockout partially block the ability of Pim/AKT inhibitors to suppress tumor growth and mTORC1 activity; knock-in of phospho-mimic S1530E confers resistance to Pim and AKT inhibitors.\",\n      \"method\": \"Phospho-specific antibodies; phospho-inactive mutant transfection; DEPDC5 knockout; phospho-mimic knock-in in tumor cells; in vitro and in vivo tumor growth assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — phosphorylation confirmed by antibodies and mutagenesis, functional consequence validated in vitro and in vivo\",\n      \"pmids\": [\"31548394\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Depdc5 loss in neurons leads to mTORC1-dependent reduction in levels of the other GATOR1 subunits NPRL2 and NPRL3; rapamycin rescues mTORC1 hyperactivation (pS6) but not GATOR1 protein levels, indicating a downstream effect on complex stability.\",\n      \"method\": \"Western blotting of GATOR1 subunits in Depdc5cc+ knockout mouse brain; rapamycin treatment\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with orthogonal protein level measurements and pharmacological rescue, single lab\",\n      \"pmids\": [\"31174205\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"DEPDC5 inactivation in GIST (gastrointestinal stromal tumor) cells reduces cell proliferation through the mTORC1 signaling pathway, induces cell-cycle arrest, and promotes tumor growth in vitro and in vivo; DEPDC5 is validated as a tumor suppressor.\",\n      \"method\": \"Whole-exome sequencing of GISTs; DEPDC5 inactivation in cell lines; DEPDC5 overexpression in vitro; nude mouse xenograft assay; mTORC1 pathway analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal functional assays (KO, OE, in vivo xenograft) with mTORC1 pathway mechanistic readouts\",\n      \"pmids\": [\"31636198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Second-hit DEPDC5 somatic mutations are restricted to dysmorphic neurons in focal cortical dysplasia IIA, and the somatic mutation load correlates with dysmorphic neuron density and the epileptogenic zone, confirming cell-autonomous mTORC1 hyperactivation drives the dysplastic phenotype.\",\n      \"method\": \"Deep sequencing of laser-captured dysmorphic neurons from human surgical tissue; correlation analysis\",\n      \"journal\": \"Annals of clinical and translational neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — cell-type-specific deep sequencing with functional correlation in human tissue\",\n      \"pmids\": [\"31353856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Acute Depdc5 knockdown (~40–80%) in primary cortical neurons causes mTOR hyperactivation, increased soma size, dendritic arborization, increased excitatory synaptic transmission (mEPSC frequency and amplitude), increased density of excitatory synapses, and glutamate receptor expression, while inhibitory synapses are unaffected—demonstrating an excitation/inhibition imbalance causally linked to Depdc5 loss.\",\n      \"method\": \"RNAi-mediated acute Depdc5 knockdown in primary cortical cultures; electrophysiology (mEPSC/mIPSC recording); immunocytochemistry for synaptic markers\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — electrophysiology combined with morphological and molecular assays, dose-dependent effect established\",\n      \"pmids\": [\"32113911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Depdc5 knockout (but not Tsc2 knockout) cells fail to reduce mTOR lysosomal localization or S6/4E-BP1 phosphorylation in amino acid-free conditions, demonstrating that DEPDC5 specifically mediates amino acid-sensing-dependent lysosomal recruitment/inactivation of mTOR in neurons.\",\n      \"method\": \"CRISPR-edited Neuro2a cells and differentiated neurons; CFP/YFP FRET-biosensor for 4E-BP1 phosphorylation; confocal imaging of mTOR lysosomal localization during amino acid starvation\",\n      \"journal\": \"Experimental neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — live-cell FRET biosensor plus confocal imaging with mechanistic comparison of Depdc5 vs Tsc2 KO\",\n      \"pmids\": [\"32781001\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Depdc5 deficiency in hepatocytes leads to mTORC1 hyperactivation and suppression of PPARα pathway, causing exacerbation of alcohol-induced hepatic steatosis; the steatotic phenotype is reversed by the mTORC1 inhibitor Torin1 or by fenofibrate (PPARα agonist), placing DEPDC5 upstream of mTORC1–PPARα axis in hepatocytes.\",\n      \"method\": \"Hepatocyte-specific Depdc5 conditional knockout mouse (Depdc5-LKO); ethanol feeding model; Torin1 and fenofibrate pharmacological rescue; liver histology and lipid measurements\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — clean conditional KO with pharmacological rescue identifying the downstream PPARα pathway\",\n      \"pmids\": [\"34267188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Brain mTORC1 signaling is reduced after acute fasting in mice; DEPDC5 (GATOR1 component) is required for neuronal mTORC1 to sense amino acid withdrawal (leucine, arginine, glutamine); neuronal Depdc5 knockout mice are resistant to amino acid fluctuations after fasting and to the seizure-protective effects of fasting, establishing DEPDC5 as the essential link between amino acid sensing and mTORC1 regulation in neurons mediating fasting-induced seizure protection.\",\n      \"method\": \"Neuronal Depdc5 conditional knockout mice; metabolomics; seizure threshold assays after fasting; leucine/arginine/glutamine deprivation assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — clean conditional KO with metabolomics and in vivo seizure readout, multiple orthogonal methods\",\n      \"pmids\": [\"36044864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Depdc5 deletion in excitatory neurons (cortical layer 5 and dentate gyrus) but not in cortical interneurons is sufficient to cause frequent generalized tonic-clonic seizures and SUDEP-like events; ictal apnea occurs before terminal cardiac asystole, and baseline respiratory dysfunction precedes SUDEP, implicating excitatory neuron-mediated respiratory dysregulation in SUDEP.\",\n      \"method\": \"Cell-type-specific Cre-lox Depdc5 knockout mice; EEG; simultaneous EEG-ECG; respiratory recordings; hypoxia challenge\",\n      \"journal\": \"Annals of neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple cell-type-specific KO lines with simultaneous multimodal physiological recordings\",\n      \"pmids\": [\"37606181\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DEPDC5 interacts with USP46 (ubiquitin-specific protease 46), WDR48, and WDR20 as binding partners; loss of DEPDC5 leads to mTORC1-dependent USP46 upregulation, decreased GluA1 ubiquitination, and increased surface GluA1-containing AMPA receptors—shifting glutamate quantal size upward and increasing excitatory synaptic strength. USP46 knockdown or rapamycin rescues this phenotype.\",\n      \"method\": \"Co-immunoprecipitation/protein interaction network analysis; Depdc5 conditional knockout mouse; electrophysiology (quantal size); ubiquitination assay; USP46 knockdown rescue; rapamycin rescue\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — interaction identified by Co-IP, mechanistic pathway established through KO + rescue with both genetic (USP46 KD) and pharmacological (rapamycin) approaches and electrophysiological readout\",\n      \"pmids\": [\"40467011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In T cell-specific Depdc5 knockout mice, DEPDC5-deficient CD8+ T cells produce high levels of xanthine oxidase and lipid ROS due to hyper-mTORC1-induced ATF4 expression, leading to spontaneous ferroptosis and reduced peripheral CD8+ T cell numbers.\",\n      \"method\": \"T cell-specific Depdc5 conditional knockout mice; ROS measurement; xanthine oxidase assay; ATF4 expression analysis; ferroptosis markers\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean conditional KO with multiple orthogonal mechanistic readouts identifying the mTORC1-ATF4-xanthine oxidase-ferroptosis axis\",\n      \"pmids\": [\"38763950\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Biallelic inactivation of Depdc5 in mouse medial prefrontal cortex leads to shared alterations in pyramidal neuron morphology, positioning, and membrane excitability compared with other mTORC1 pathway gene knockouts, but causes gene-specific differences in excitatory synaptic transmission.\",\n      \"method\": \"In utero electroporation for biallelic inactivation; patch-clamp electrophysiology; morphological analysis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct in vivo manipulation with electrophysiology and morphological readouts, comparator design across multiple genes\",\n      \"pmids\": [\"38411613\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DEPDC5 down-regulation in hepatic stellate cells leads to increased β-catenin expression and production of MMP2 (matrix metallopeptidase 2), a secreted enzyme involved in fibrosis progression, identifying a DEPDC5–β-catenin–MMP2 pathway in hepatic stellate cells distinct from mTORC1.\",\n      \"method\": \"DEPDC5 siRNA knockdown in immortalized hepatic stellate cells (LX-2); β-catenin and MMP2 expression assays\",\n      \"journal\": \"Hepatology (Baltimore, Md.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single in vitro knockdown experiment, single lab, no rescue or mechanistic follow-up\",\n      \"pmids\": [\"26517016\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DEPDC5 knockout in hepatocellular carcinoma cells leads to resistance to leucine starvation via impaired autophagy (reduced LC3-II, p62 accumulation, and ROS tolerance); DEPDC5 overexpression suppresses cell proliferation and tumorigenicity in immunocompromised mice, and promotes p62 degradation with increased ROS susceptibility.\",\n      \"method\": \"CRISPR/Cas9 DEPDC5 knockout in HCC cells; LC3-II/p62 western blotting; ROS assay; xenograft mouse model\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — CRISPR KO and OE with in vitro and in vivo readouts, single lab\",\n      \"pmids\": [\"29311600\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Focal perineuronal net (PNN) degradation by proteolytic enzymes occurs in the malformed cortex of forebrain Depdc5-knockout mice prior to seizures, coincident with microglia inflammation, resulting in parvalbumin interneuron loss and impaired presynaptic inhibition.\",\n      \"method\": \"Forebrain-specific Depdc5 conditional knockout mouse; immunohistochemistry for PNNs (WFA staining), parvalbumin, and microglial markers; electrophysiology\",\n      \"journal\": \"Developmental neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO with immunohistochemical and electrophysiological readouts, single lab, non-cell-autonomous mechanism identified\",\n      \"pmids\": [\"35580549\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DEPDC5 protein degradation in colorectal cancer is mediated through chaperone-mediated autophagy (CMA) downstream of the GPR81/lactate signaling axis; SNX10 interacts with DEPDC5 and recruits it to lysosomes for CMA-mediated degradation, activating mTORC1 and promoting EMT and metastasis.\",\n      \"method\": \"siRNA knockdown; Co-IP demonstrating SNX10-DEPDC5 interaction; western blotting for CMA markers; in vivo lung metastasis mouse model\",\n      \"journal\": \"Phytomedicine : international journal of phytotherapy and phytopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP showing interaction plus functional knockdown, in vivo model; single lab\",\n      \"pmids\": [\"38615493\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A DEPDC5 missense variant (p.Phe685Leu) causes altered subcellular localization of the mutant protein in primary neurons and, when knocked into mice (hDEPDC5F685L), produces mTOR hyperactivation, enlarged neuronal soma, abnormal neurons, and heightened seizure susceptibility; rapamycin rescues neuronal size and mTOR activity and reduces seizure susceptibility.\",\n      \"method\": \"Mutant plasmid transfection for localization; nervous system-specific knock-in mouse; immunohistochemistry; seizure threshold assays; rapamycin rescue\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — knock-in mouse with localization data and pharmacological rescue, multiple readouts\",\n      \"pmids\": [\"39954744\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Postnatal focal cortical DEPDC5 loss (without disrupting embryonic cortical migration) is sufficient to cause mTOR hyperactivation, FCD pathological hallmarks (increased SMI-311 neurofilament, hypomyelination, astrogliosis, microglial activation), lowered seizure thresholds, increased focal seizures, and increased seizure-induced death, demonstrating a cell-autonomous postnatal role of DEPDC5.\",\n      \"method\": \"Postnatal AAV-Cre injection in floxed Depdc5 mice; histopathology; EEG; seizure threshold assays\",\n      \"journal\": \"JCI insight\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean focal postnatal KO with multiple histopathological and electrophysiological readouts\",\n      \"pmids\": [\"40996830\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Mosaic biallelic DEPDC5 two-hit inactivation in human cortical organoids (hCOs) causes increased mTOR activity (rescued by rapamycin), dysmorphic-like neurons, enhanced neuronal excitability, premature upper-layer neuron generation, dysregulated Notch and Wnt signaling in neural progenitors, and altered metabolism and translation—establishing cell-autonomous effects of DEPDC5 biallelic loss during human corticogenesis.\",\n      \"method\": \"Patient-derived human cortical organoids with mosaic DEPDC5 two-hit deletion; single-cell transcriptomics; electrophysiology; rapamycin rescue; immunofluorescence\",\n      \"journal\": \"Brain : a journal of neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — human organoid model with single-cell transcriptomics, electrophysiology, and pharmacological rescue\",\n      \"pmids\": [\"41789478\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DEPDC5 is a core subunit of the GATOR1 complex (together with NPRL2 and NPRL3) that functions as a GTPase-activating protein (GAP) toward RagA/B GTPases, acting as the primary amino acid–sensing brake on lysosomal mTORC1 recruitment and activation; loss of DEPDC5 causes constitutive mTORC1 hyperactivation that drives neuronal soma enlargement, dysplastic morphology, altered dendritic/synaptic structure, excitation–inhibition imbalance (via USP46-mediated GluA1 deubiquitination and AMPA receptor surface accumulation), and focal cortical dysplasia-associated epilepsy, while upstream Pim1/AKT kinases can phosphorylate DEPDC5 to release this inhibition, and DEPDC5 also controls CD8+ T cell ferroptosis via an mTORC1–ATF4–xanthine oxidase axis.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"DEPDC5 is a core subunit of the GATOR1 complex that functions as the principal amino acid–sensing negative regulator of mTORC1, controlling lysosomal mTOR recruitment and activity via GTPase-activating protein function toward RagA/B GTPases. DEPDC5 loss abolishes mTORC1 suppression during amino acid withdrawal, causing constitutive mTORC1 hyperactivation that drives neuronal soma enlargement, dendritic dysmorphology, increased excitatory synaptic strength—including mTORC1-dependent USP46 upregulation leading to GluA1 deubiquitination and AMPA receptor surface accumulation—and excitation–inhibition imbalance [PMID:23542697, PMID:32781001, PMID:32113911, PMID:40467011]. Germline heterozygous DEPDC5 loss-of-function mutations combined with somatic second-hit inactivation cause focal cortical dysplasia and mTORC1-dependent epilepsy with SUDEP, where excitatory neuron loss drives respiratory dysregulation preceding terminal cardiac events [PMID:29708508, PMID:31353856, PMID:37606181]. Beyond neurons, DEPDC5 is phosphorylated by Pim1/AKT to release GATOR1-mediated mTORC1 inhibition in cancer cells, functions as a tumor suppressor in gastrointestinal stromal tumors, regulates hepatocyte PPARα-dependent lipid metabolism, and controls CD8+ T cell ferroptosis through an mTORC1–ATF4–xanthine oxidase axis [PMID:31548394, PMID:31636198, PMID:34267188, PMID:38763950].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Identifying DEPDC5 as a GATOR1 subunit and mTORC1 repressor answered what molecular complex mediates amino acid–dependent mTORC1 inhibition and linked its loss-of-function to familial focal epilepsy.\",\n      \"evidence\": \"Exome sequencing in epilepsy families combined with functional mTORC1 signaling assays\",\n      \"pmids\": [\"23542697\", \"23542701\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"GAP activity toward Rag GTPases not yet directly demonstrated\", \"structural basis of GATOR1 complex assembly unknown\", \"mechanism linking mTORC1 hyperactivation to seizures uncharacterized\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Systematic functional testing of epilepsy-associated DEPDC5 variants established that specific mutations disrupt GATOR1 complex integrity and/or mTORC1 inhibitory function, validating a loss-of-function mechanism for disease alleles.\",\n      \"evidence\": \"In vitro mTORC1 signaling and GATOR1 complex formation assays on 10 epilepsy-associated and 2 tumor-associated DEPDC5 variants\",\n      \"pmids\": [\"25366275\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"structural basis of variant-specific disruption unknown\", \"genotype–phenotype correlation for seizure severity not established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"In vivo genetic ablation in rodents demonstrated that DEPDC5 is essential for embryonic viability and that constitutive mTORC1 hyperactivation is the causal downstream mechanism, as rapamycin rescued embryonic lethality.\",\n      \"evidence\": \"TALEN-generated Depdc5 knockout rat with mTORC1 phosphorylation assays and prenatal rapamycin rescue\",\n      \"pmids\": [\"26873552\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"cell-type-specific requirements not yet dissected\", \"whether mTORC1 is the sole effector of DEPDC5 loss not excluded\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Neuron-specific conditional knockout resolved that DEPDC5 loss in neurons—not glia—drives mTORC1 hyperactivation, cortical dysplasia, and seizures, establishing cell-autonomous neuronal pathology.\",\n      \"evidence\": \"Syn1-Cre conditional Depdc5 knockout mouse with EEG, pS6 immunohistochemistry, and seizure threshold assays\",\n      \"pmids\": [\"29274432\", \"28974734\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"which neuronal subtypes are most vulnerable not determined\", \"downstream effectors mediating seizure generation unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstration that biallelic (germline + somatic second-hit) DEPDC5 inactivation is required for focal cortical dysplasia, and that focal somatic deletion alone recapitulates FCD and SUDEP in rodents, established the two-hit model and cell-autonomous sufficiency of DEPDC5 loss for epileptogenesis.\",\n      \"evidence\": \"Deep sequencing of human surgical tissue; CRISPR/in utero electroporation in mouse and rat; neuromorphological and EEG analysis\",\n      \"pmids\": [\"29708508\", \"30080265\", \"31353856\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"timing of second-hit relative to cortical development not defined\", \"whether migration defects are required for epileptogenesis unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Mechanistic dissection in neuronal cells showed DEPDC5 specifically controls amino acid–dependent lysosomal mTOR recruitment (distinct from TSC2/Rheb axis), explaining why DEPDC5 loss causes mTORC1 hyperactivation even during amino acid starvation.\",\n      \"evidence\": \"CRISPR Depdc5 vs Tsc2 knockout in Neuro2a cells; FRET biosensor for 4E-BP1 phosphorylation; confocal imaging of mTOR–lysosome colocalization\",\n      \"pmids\": [\"32781001\", \"29481864\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"direct GAP activity measurement on Rag GTPases in neuronal context not performed\", \"whether nutrient-independent functions of DEPDC5 exist in neurons not addressed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Discovery that Pim1 and AKT phosphorylate DEPDC5 to release GATOR1-mediated mTORC1 inhibition established DEPDC5 as a signal-regulated node integrating growth factor and amino acid sensing, with direct therapeutic implications for kinase inhibitor resistance in cancer.\",\n      \"evidence\": \"Phospho-specific antibodies; phospho-inactive and phospho-mimic DEPDC5 mutants; DEPDC5 knockout tumor cells; in vivo xenograft assays\",\n      \"pmids\": [\"31548394\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"phosphorylation sites not mapped at residue resolution beyond S1530\", \"whether phosphorylation affects GATOR1 complex integrity or GAP activity not distinguished\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Electrophysiological characterization revealed that DEPDC5 loss selectively increases excitatory but not inhibitory synaptic transmission, directly demonstrating that excitation–inhibition imbalance is a proximal mechanism of DEPDC5-associated epileptogenesis.\",\n      \"evidence\": \"Acute RNAi knockdown in primary cortical neurons; mEPSC/mIPSC recordings; synaptic marker immunocytochemistry\",\n      \"pmids\": [\"32113911\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"molecular identity of upregulated glutamate receptors not fully characterized\", \"contribution of presynaptic vs postsynaptic mechanisms not resolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Establishing that neuronal DEPDC5 is required for mTORC1 to sense amino acid fluctuations during fasting—and that this sensing mediates fasting-induced seizure protection—linked DEPDC5's metabolic function to a clinically relevant anticonvulsant mechanism.\",\n      \"evidence\": \"Neuronal Depdc5 conditional knockout mice; metabolomics; seizure threshold assays after fasting; specific amino acid deprivation experiments\",\n      \"pmids\": [\"36044864\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"which specific amino acid sensors upstream of GATOR1 are active in neurons not identified\", \"whether dietary interventions can substitute for DEPDC5 function not tested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Cell-type-specific knockout showed that DEPDC5 loss in excitatory (but not inhibitory) neurons is sufficient for seizures and SUDEP, with ictal apnea preceding cardiac arrest, identifying respiratory circuit dysfunction as the proximal cause of SUDEP.\",\n      \"evidence\": \"Multiple Cre-driver Depdc5 knockout lines; simultaneous EEG-ECG-respiratory recordings; hypoxia challenge\",\n      \"pmids\": [\"37606181\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"specific brainstem circuits mediating respiratory failure not identified\", \"whether interventions targeting respiratory drive can prevent SUDEP not tested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identification of USP46 as a DEPDC5-interacting deubiquitinase revealed the molecular mechanism by which DEPDC5 loss increases excitatory synaptic strength: mTORC1-dependent USP46 upregulation reduces GluA1 ubiquitination, increasing surface AMPA receptors and glutamate quantal size.\",\n      \"evidence\": \"Co-immunoprecipitation; Depdc5 conditional knockout; GluA1 ubiquitination assay; electrophysiology; USP46 knockdown and rapamycin rescue\",\n      \"pmids\": [\"40467011\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"whether USP46 pathway is sufficient to explain all excitatory synaptic changes not established\", \"reciprocal Co-IP for DEPDC5–USP46 not explicitly described\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"DEPDC5's role was extended beyond neurons: in CD8+ T cells, DEPDC5 loss causes hyper-mTORC1–driven ATF4 upregulation, xanthine oxidase production, lipid ROS accumulation, and spontaneous ferroptosis, establishing DEPDC5 as an immune cell survival factor.\",\n      \"evidence\": \"T cell–specific Depdc5 conditional knockout mice; ROS and xanthine oxidase assays; ATF4 expression; ferroptosis markers\",\n      \"pmids\": [\"38763950\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"whether DEPDC5-dependent ferroptosis occurs in other immune cell types unknown\", \"therapeutic relevance of modulating this axis in immunotherapy not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Postnatal focal DEPDC5 deletion demonstrated that cortical dysplasia and epilepsy can arise independently of embryonic migration defects, and a patient-derived missense knock-in confirmed that subcellular mislocalization of mutant DEPDC5 is sufficient for mTOR hyperactivation and seizure susceptibility.\",\n      \"evidence\": \"Postnatal AAV-Cre in floxed Depdc5 mice; knock-in mouse of hDEPDC5-F685L; rapamycin rescue; EEG and histopathology\",\n      \"pmids\": [\"40996830\", \"39954744\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"window of postnatal vulnerability not defined\", \"structural basis of missense-induced mislocalization unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Human cortical organoids with mosaic biallelic DEPDC5 loss recapitulated dysmorphic neurons, hyperexcitability, and premature upper-layer neurogenesis with dysregulated Notch/Wnt signaling, establishing cell-autonomous human-specific developmental consequences of DEPDC5 loss.\",\n      \"evidence\": \"Patient-derived cortical organoids with mosaic two-hit DEPDC5 deletion; single-cell transcriptomics; electrophysiology; rapamycin rescue\",\n      \"pmids\": [\"41789478\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"whether Notch/Wnt dysregulation is mTORC1-dependent or independent not resolved\", \"organoid model lacks circuit-level validation\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Major open questions include the direct structural basis of DEPDC5's GAP activity toward Rag GTPases, identification of upstream amino acid sensors feeding into GATOR1 in neurons, whether non-mTORC1 functions of DEPDC5 contribute to disease, and whether targeting the USP46–GluA1 axis or ferroptosis pathway has therapeutic potential.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"no reconstituted GAP assay for human DEPDC5 on Rag GTPases\", \"upstream amino acid sensors in neurons not identified\", \"therapeutic window for postnatal intervention not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 3, 10, 11]},\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 10, 16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [7, 16, 26]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [7, 27]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 3, 10, 11, 16, 18]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [24]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [4, 6, 15, 19, 20, 22]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [21]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [21]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [13, 26]}\n    ],\n    \"complexes\": [\n      \"GATOR1\"\n    ],\n    \"partners\": [\n      \"NPRL2\",\n      \"NPRL3\",\n      \"USP46\",\n      \"WDR48\",\n      \"WDR20\",\n      \"SNX10\",\n      \"RRAGA\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}