{"gene":"PDPK1","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2010,"finding":"Genetic knockout of PDPK1 in human colorectal cancer cells reduces GSK3β and mTOR activation, whereas AKT1/AKT2 double knockout affects FOXO proteins but not GSK3β or mTOR, placing PDPK1 upstream of GSK3β and mTOR in a pathway distinct from AKT in this context.","method":"Targeted homologous recombination knockout in human colon cancer cell lines; downstream signaling assessed by western blot","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic KO with defined downstream signaling readouts, replicated across multiple cell lines, orthogonal to AKT KO results","pmids":["20133737"],"is_preprint":false},{"year":2014,"finding":"PDPK1 phosphorylates and activates RSK2, AKT, c-MYC, IRF4, and cyclin Ds in multiple myeloma cells; PDPK1 inhibition induces apoptosis via activation of BIM and BAD.","method":"Pharmacological inhibition and siRNA knockdown of PDPK1 in multiple myeloma cell lines; western blot for downstream substrates and apoptotic markers","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined molecular readouts, single lab, two orthogonal methods (inhibitor + siRNA)","pmids":["25269480"],"is_preprint":false},{"year":2017,"finding":"Chlamydia trachomatis infection activates PDPK1 signaling, which phosphorylates and stabilizes MYC; PDPK1-MYC signaling induces hexokinase II (HKII) expression and HKII translocation/enrichment at mitochondria to prevent apoptosis of infected cells.","method":"Biochemical approaches (co-immunoprecipitation, western blot), imaging, pharmacological inhibition of PDPK1 and MYC, exogenous peptides blocking HKII-mitochondria interaction","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biochemical and imaging methods in single lab establishing the PDPK1-MYC-HKII axis","pmids":["28803120"],"is_preprint":false},{"year":2011,"finding":"The MID1 ubiquitin ligase complex associates with PDPK1 mRNA via a purine-rich MIDAS sequence motif, increasing its translational efficiency; PDPK1 protein synthesis is significantly reduced in cells from Opitz syndrome patients with mutated MID1 and can be rescued by functional MID1.","method":"mRNA co-immunoprecipitation, translational efficiency assays, patient-derived cell comparison, MID1 rescue experiments","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (co-IP, reporter assay, patient cells, rescue), single lab","pmids":["21930711"],"is_preprint":false},{"year":2020,"finding":"PDPK1 SUMOylation at lysine 299 (within the kinase domain) is required for its autophosphorylation at serine 241 and subsequent activation of AKT1-MTOR signaling; SUMOylation of PDPK1 is inhibited by binding to PIK3C3, and non-SUMOylated PDPK1 tethers LC3 to the ER to initiate autophagosome biogenesis.","method":"Co-immunoprecipitation, site-directed mutagenesis (K299), in vivo SUMOylation assays, autophagy detection (LC3 localization), biochemical fractionation","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods including mutagenesis and co-IP, single lab","pmids":["32876514"],"is_preprint":false},{"year":2019,"finding":"Avibirnavirus VP3 CC3 domain disrupts the PIK3C3-PDPK1 complex by directly binding to PIK3C3; release of PDPK1 from PIK3C3 allows PDPK1 to activate the AKT-MTOR pathway, suppressing autophagy to facilitate viral replication.","method":"Co-immunoprecipitation, domain mapping, autophagy assays, viral replication assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with domain mapping establishing direct interaction, single lab","pmids":["31885313"],"is_preprint":false},{"year":2022,"finding":"UBC9-mediated SUMOylation of PDPK1 at lysine 299 is required for PDPK1 autophosphorylation at serine 241 and downstream mTORC1 activation; loss of PDPK1 SUMOylation impairs CD4 T-cell glycolytic metabolism and homeostatic proliferation.","method":"SUMOylation site mutagenesis (K299), autophosphorylation assays, mTORC1 activity assays, T-cell proliferation and glycolysis assays in vivo and in vitro","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — mutagenesis identifying specific SUMOylation site plus functional readouts, single lab","pmids":["35210408"],"is_preprint":false},{"year":2024,"finding":"Coronavirus M protein recruits PDPK1 to phosphorylate SQSTM1 (p62) at threonine 138, directing autophagy substrate selection from virophagy toward mitophagy, thereby suppressing innate immunity and promoting viral replication.","method":"Dual split-fluorescence assay, site-directed mutagenesis (T138), co-immunoprecipitation, viral replication assays, PDPK1-targeting peptide inhibition, mouse infection model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — mutagenesis identifying phosphorylation site, multiple orthogonal methods (fluorescence assay, co-IP, peptide inhibitor, in vivo model), single lab with rigorous controls","pmids":["39414765"],"is_preprint":false},{"year":2020,"finding":"PDPK1 mediates prostate cancer cell survival predominantly via phosphorylation and activation of SGK3; PDPK1 knockdown reduces SGK3 phosphorylation, induces apoptosis, and constitutively active SGK3 rescues apoptosis caused by PDPK1 loss, while AKT and SGK1 phosphorylation were not affected.","method":"shRNA knockdown, ectopic expression of constitutively active SGK3, western blot for phosphorylation status, apoptosis assays","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis via rescue experiment, two orthogonal approaches (KD + OE), single lab","pmids":["32926495"],"is_preprint":false},{"year":2015,"finding":"Physical interaction between AKT1 and PDPK1 is required for AKT1 activation; a small molecule inhibitor (NSC156529) that specifically disrupts the AKT1-PDPK1 interaction downregulates AKT1 signaling, decreases cancer cell proliferation in vitro, and inhibits prostate tumor xenograft growth in vivo.","method":"Live cell-based screen for protein-protein interaction inhibitors, western blot for AKT1 phosphorylation, cell proliferation assays, in vivo xenograft model","journal":"Molecular cancer therapeutics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interaction-based mechanism validated with functional readouts in vitro and in vivo, single lab","pmids":["26294745"],"is_preprint":false},{"year":2017,"finding":"ARL15 knockdown specifically inhibits PDPK1 phosphorylation at Ser241, thereby reducing PDPK1 activity and downstream AKT Thr308 phosphorylation in the insulin signaling pathway; ARL15 interacts with ASAP2 (a GAP for ARL15) as identified by co-immunoprecipitation.","method":"ARL15 overexpression and knockdown in C2C12 myotubes, western blot for PDPK1-S241 and AKT-T308 phosphorylation, co-immunoprecipitation for ARL15-ASAP2 interaction","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single co-IP and western blot methods without reconstitution or mutagenesis","pmids":["28322786"],"is_preprint":false},{"year":2024,"finding":"AQP3 accumulation (caused by FBXW5 knockdown) induces lysosomal-dependent degradation of PDPK1, thereby inactivating the AKT-MTOR pathway and inducing autophagic cell death in hepatocellular carcinoma cells.","method":"FBXW5 knockdown, AQP3 overexpression/knockdown, lysosomal inhibition, western blot for PDPK1 and AKT-MTOR pathway components, autophagy assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple genetic perturbations with defined molecular mechanism, single lab, orthogonal pathway validation","pmids":["38726865"],"is_preprint":false},{"year":2022,"finding":"LIFR-K620 acetylation facilitates LIFR homodimerization and LIFR-S1044 phosphorylation, which recruits PDPK1 to activate AKT signaling; PDPK1 in turn enhances GCN5 protein level, forming a positive feedback loop sustaining LIFR-K620 acetylation.","method":"Liquid mass spectrometry, genetically engineered mouse models, organoid assays, co-immunoprecipitation, lentiviral constructs","journal":"Clinical and translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods including mass spectrometry and GEM models, single lab","pmids":["35172032"],"is_preprint":false},{"year":2026,"finding":"SENP3 directly interacts with PDPK1 (identified by co-immunoprecipitation/mass spectrometry), promotes PDPK1 deSUMOylation at Lys296, leading to increased K48-linked ubiquitination and proteasomal degradation of PDPK1, thereby suppressing PI3K-AKT signaling and inducing apoptosis during intestinal ischemia/reperfusion.","method":"Immunoprecipitation-mass spectrometry, co-immunoprecipitation, site-directed mutagenesis (K296), ubiquitination assays, SENP3 knockdown, western blot for PI3K-AKT pathway","journal":"Biochemical pharmacology","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — mutagenesis identifying SUMOylation site, mass spectrometry interaction discovery, multiple orthogonal methods, single lab","pmids":["42140449"],"is_preprint":false},{"year":2024,"finding":"CPT1A mediates succinylation of SP5, which strengthens SP5 binding to the PDPK1 promoter and activates PDPK1 transcription; elevated PDPK1 then activates AKT/mTOR signaling to promote prostate cancer cell viability and glycolysis.","method":"Luciferase reporter assay, ChIP assay, co-immunoprecipitation, CCK-8, Seahorse glycolysis assay","journal":"Cancer biology & therapy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and luciferase assays establishing transcriptional mechanism, co-IP for protein interaction, single lab","pmids":["38494680"],"is_preprint":false},{"year":2024,"finding":"N-MYC physically interacts with PDPK1 through the WDR5-PDPK1 interaction in neuroblastoma cells; PDPK1 and N-MYC co-regulate a specific set of genes involved in spindle pole formation and chromosome segregation, overlapping with WDR5-regulated genes, suggesting a tripartite N-MYC-WDR5-PDPK1 complex regulates mitotic gene expression.","method":"RNA-seq transcriptomic analysis, co-immunoprecipitation for N-MYC-PDPK1 physical interaction, comparative analysis with WDR5 inhibition data","journal":"BMC genomics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single co-IP for physical interaction, transcriptomic analysis for gene regulation, single lab, limited functional validation","pmids":["38605297"],"is_preprint":false},{"year":2019,"finding":"Vascular endothelial-specific deletion of PDPK1 (Tie2-Cre) reduces islet blood flow, decreases endothelial fenestration, causes hypoxia in islets, and leads to reduced pancreatic beta cell mass and impaired glucose-stimulated insulin secretion, demonstrating a role for endothelial PDPK1 in maintaining islet vascularity and beta cell function.","method":"Conditional knockout mice (Tie2+/-/Pdpk1flox/flox), glucose tolerance tests, insulin secretion assays, microsphere islet blood flow measurement, immunohistochemistry, electron microscopy","journal":"Diabetologia","confidence":"High","confidence_rationale":"Tier 2 / Strong — rigorous conditional KO with multiple orthogonal readouts (functional, histological, molecular), well-controlled mouse model","pmids":["31055616"],"is_preprint":false},{"year":2026,"finding":"PDPK1 activates NFKB1, which transactivates the anti-apoptotic gene BIRC3; BIRC3 overexpression reverses pro-apoptotic effects of PDPK1 knockdown, establishing PDPK1/NFKB1/BIRC3 as a signaling axis driving radiotherapy resistance in lung adenocarcinoma.","method":"ChIP assay, dual-luciferase assay, RNA sequencing, siRNA knockdown, BIRC3 overexpression rescue, colony formation and apoptosis assays","journal":"Cancer cell international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and luciferase establishing direct transcriptional regulation, genetic epistasis via rescue, single lab","pmids":["41862915"],"is_preprint":false},{"year":2025,"finding":"PDPK1 co-expressed with RPS6KB1 (p70S6K1) in a baculovirus system phosphorylates and activates p70S6K1, confirming PDPK1 as a direct upstream kinase of p70S6K1; a PH-domain-deleted PDPK1 construct was sufficient for this activity.","method":"Baculovirus dual expression system, Kinase-Glo assay, AlphaScreen kinase assay, immunoblotting","journal":"Molecular biology reports","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro reconstitution of kinase activity with validated assays, single lab, no mutagenesis of active site","pmids":["39821712"],"is_preprint":false},{"year":2021,"finding":"In small-cell lung cancer cells, PDPK1 and Akt affect Hedgehog pathway expression (PDPK1 silencing reduces Hedgehog expression), but Hedgehog does not affect PDPK1 or p-Akt expression, placing PDPK1-Akt upstream of Hedgehog signaling.","method":"siRNA transfection for PDPK1 and Akt silencing, pharmacological Hedgehog inhibition, proliferation and migration assays, western blot","journal":"The Journal of international medical research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — genetic epistasis by single-gene knockdown, single lab, no reconstitution or direct interaction data","pmids":["34038205"],"is_preprint":false},{"year":2026,"finding":"PDPK1 directly binds penfluridol (demonstrated by drug affinity responsive target stability assay); penfluridol inhibits PDPK1 kinase activity and reduces AKT1 phosphorylation, which decreases CTR1 ubiquitination, stabilizes CTR1 on the plasma membrane, and promotes intracellular copper accumulation leading to cuproptosis in colorectal cancer.","method":"Drug affinity responsive target stability (DARTS) assay, PDPK1 kinase activity assay, ubiquitination assay, western blot for p-AKT1 and CTR1, patient-derived organoids, PDX model","journal":"Acta pharmacologica Sinica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct drug-target binding confirmed by DARTS, kinase activity measured, multiple model systems, single lab","pmids":["42185682"],"is_preprint":false}],"current_model":"PDPK1 is a serine/threonine kinase that occupies a central node in PI3K signaling: it directly phosphorylates and activates multiple AGC-family kinases (AKT at T308, SGK3, RSK2, S6K/p70S6K1) to regulate cell survival, growth, glycolysis, and autophagy; its activity is governed by post-translational modifications including SUMOylation at K299 (required for autophosphorylation at S241 and mTORC1 activation) and deSUMOylation by SENP3 at K296 (which triggers K48-ubiquitination and proteasomal degradation); it forms regulated complexes with PIK3C3 (VPS34), AKT1, and WDR5/N-MYC that control autophagosome biogenesis and mitotic gene expression; it phosphorylates SQSTM1-T138 to direct autophagy cargo selection; and in endothelial cells it maintains pancreatic islet vascularity and beta cell function in vivo."},"narrative":{"mechanistic_narrative":"PDPK1 is a serine/threonine kinase that occupies a central node in PI3K-AKT/mTOR signaling, transducing growth, survival, and metabolic cues by directly phosphorylating and activating multiple AGC-family kinases [PMID:25269480, PMID:32926495, PMID:39821712]. It activates AKT through a required physical interaction, and disrupting the AKT1-PDPK1 interface with a small molecule downregulates AKT signaling and tumor growth [PMID:26294745]; in distinct cellular contexts it selectively routes survival signaling through SGK3 in prostate cancer [PMID:32926495], through RSK2, c-MYC, IRF4, and cyclin Ds in multiple myeloma [PMID:25269480], and directly phosphorylates p70S6K1 in vitro [PMID:39821712]. Genetically, PDPK1 lies upstream of GSK3β and mTOR in a branch distinct from AKT-FOXO signaling [PMID:20133737]. PDPK1 activity is gated by SUMOylation at K299 by UBC9, which is required for its S241 autophosphorylation and downstream mTORC1 activation, supporting glycolytic metabolism and T-cell proliferation [PMID:35210408, PMID:32876514]; deSUMOylation at K296 by SENP3 triggers K48-ubiquitination and proteasomal degradation, suppressing PI3K-AKT signaling [PMID:42140449]. PDPK1 also controls autophagy: binding to PIK3C3 (VPS34) inhibits its SUMOylation, and non-SUMOylated PDPK1 tethers LC3 to the ER to initiate autophagosome biogenesis [PMID:32876514], while PDPK1 phosphorylation of SQSTM1/p62 at T138 directs autophagy cargo selection — a mechanism hijacked by coronavirus M protein to shift virophagy toward mitophagy and suppress innate immunity [PMID:39414765]. In vivo, vascular endothelial-specific deletion of PDPK1 reduces islet blood flow and beta cell mass and impairs glucose-stimulated insulin secretion [PMID:31055616].","teleology":[{"year":2010,"claim":"Established that PDPK1 sits upstream of GSK3β and mTOR in a signaling branch genetically separable from AKT, refining its position in the PI3K pathway.","evidence":"Targeted homologous-recombination knockout in human colon cancer lines with downstream signaling readouts, compared against AKT1/AKT2 double knockout","pmids":["20133737"],"confidence":"High","gaps":["Does not identify the direct AKT-independent substrate linking PDPK1 to GSK3β/mTOR","Context restricted to colorectal cancer cells"]},{"year":2011,"claim":"Showed PDPK1 expression is translationally regulated, linking its protein synthesis to the MID1 ubiquitin ligase complex and Opitz syndrome.","evidence":"mRNA co-immunoprecipitation, translational efficiency assays, patient-derived cells, and MID1 rescue","pmids":["21930711"],"confidence":"Medium","gaps":["MIDAS motif binding mechanism on PDPK1 mRNA not structurally defined","Does not establish kinase-pathway consequences of altered PDPK1 levels in patients"]},{"year":2014,"claim":"Demonstrated PDPK1 drives survival in multiple myeloma by activating a broad set of substrates (RSK2, AKT, c-MYC, IRF4, cyclin Ds), positioning it as a pro-survival therapeutic node.","evidence":"Pharmacological inhibition plus siRNA knockdown with apoptotic and substrate readouts","pmids":["25269480"],"confidence":"Medium","gaps":["Which substrate phosphorylations are direct versus indirect not resolved","Single disease context"]},{"year":2015,"claim":"Defined the AKT1-PDPK1 physical interaction as required for AKT1 activation and druggable, establishing protein-protein interaction disruption as an anti-tumor strategy.","evidence":"Live-cell PPI inhibitor screen (NSC156529), phospho-AKT westerns, proliferation and xenograft assays","pmids":["26294745"],"confidence":"Medium","gaps":["Interaction interface not structurally mapped","Inhibitor specificity beyond the AKT1-PDPK1 interface not fully excluded"]},{"year":2017,"claim":"Linked PDPK1 to pathogen-driven metabolic rewiring, showing a PDPK1-MYC-HKII axis prevents apoptosis of Chlamydia-infected cells.","evidence":"Co-IP, imaging, pharmacological inhibition, and HKII-mitochondria blocking peptides in infected cells","pmids":["28803120"],"confidence":"Medium","gaps":["Whether PDPK1 phosphorylates MYC directly not established","Upstream activator of PDPK1 during infection unclear"]},{"year":2019,"claim":"Revealed PDPK1's autophagy-regulatory role and its control by VPS34 binding, with a viral protein exploiting the PIK3C3-PDPK1 complex to suppress autophagy.","evidence":"Reciprocal co-IP with domain mapping of avibirnavirus VP3, plus autophagy and viral replication assays","pmids":["31885313"],"confidence":"Medium","gaps":["Direct PIK3C3-PDPK1 binding interface on PDPK1 not mapped","Endogenous (non-viral) regulator of complex dissociation unknown"]},{"year":2019,"claim":"Provided in vivo evidence that endothelial PDPK1 maintains pancreatic islet vascularity and beta cell function, extending PDPK1 biology to organismal metabolic physiology.","evidence":"Tie2-Cre conditional knockout mice with glucose tolerance, insulin secretion, islet blood flow, IHC, and EM","pmids":["31055616"],"confidence":"High","gaps":["Endothelial substrate of PDPK1 mediating fenestration not identified","Cell-autonomous beta cell role not addressed by this model"]},{"year":2020,"claim":"Identified SUMOylation at K299 as a switch governing PDPK1 autophosphorylation and bifurcating its output between mTOR activation and ER-tethered autophagosome initiation.","evidence":"K299 mutagenesis, in vivo SUMOylation assays, co-IP with PIK3C3, and LC3 localization/fractionation","pmids":["32876514"],"confidence":"Medium","gaps":["SUMO ligase responsible not identified in this study","Structural basis of how K299 SUMOylation enables S241 autophosphorylation unknown"]},{"year":2020,"claim":"Established SGK3, rather than AKT, as the dominant PDPK1 effector for survival in prostate cancer, demonstrating context-specific substrate selection.","evidence":"shRNA knockdown with constitutively active SGK3 rescue and apoptosis readouts","pmids":["32926495"],"confidence":"Medium","gaps":["What determines SGK3 versus AKT preference in this context not defined","Single cancer type"]},{"year":2022,"claim":"Assigned the SUMO E2 UBC9 to PDPK1 K299 SUMOylation and connected this modification to immune-cell glycolysis and homeostatic proliferation.","evidence":"K299 mutagenesis, autophosphorylation and mTORC1 assays, and CD4 T-cell proliferation/glycolysis in vivo and in vitro","pmids":["35210408"],"confidence":"Medium","gaps":["E3 SUMO ligase still not defined","Physiological signal triggering UBC9-PDPK1 SUMOylation unknown"]},{"year":2022,"claim":"Placed PDPK1 in a positive feedback loop with LIFR signaling, where LIFR-S1044 phosphorylation recruits PDPK1 to activate AKT and PDPK1 reinforces LIFR acetylation via GCN5.","evidence":"Mass spectrometry, co-IP, GEM models, and organoids","pmids":["35172032"],"confidence":"Medium","gaps":["Mechanism by which PDPK1 raises GCN5 levels unclear","Direct PDPK1 substrate in the loop not pinpointed"]},{"year":2024,"claim":"Showed PDPK1 directs autophagy cargo selection by phosphorylating SQSTM1/p62 at T138, a step coronavirus M protein hijacks to switch virophagy to mitophagy and evade innate immunity.","evidence":"Dual split-fluorescence, T138 mutagenesis, co-IP, peptide inhibitor, and mouse infection model","pmids":["39414765"],"confidence":"High","gaps":["How T138 phosphorylation mechanistically biases cargo recognition not fully resolved","Endogenous (non-viral) signals recruiting PDPK1 to p62 unknown"]},{"year":2024,"claim":"Demonstrated lysosomal-dependent degradation of PDPK1 as a tumor-suppressive route, with AQP3 accumulation inactivating AKT-mTOR and triggering autophagic cell death.","evidence":"FBXW5 knockdown, AQP3 modulation, lysosomal inhibition, and AKT-mTOR/autophagy readouts in HCC cells","pmids":["38726865"],"confidence":"Medium","gaps":["Direct molecular link between AQP3 and PDPK1 degradation not defined","Whether AQP3 binds PDPK1 directly unknown"]},{"year":2024,"claim":"Showed PDPK1 transcription is driven by SP5, itself controlled by CPT1A-mediated succinylation, connecting metabolic enzyme activity to PDPK1-AKT/mTOR-driven glycolysis.","evidence":"Luciferase reporter, ChIP, co-IP, and Seahorse glycolysis assays in prostate cancer cells","pmids":["38494680"],"confidence":"Medium","gaps":["Generality of SP5-driven PDPK1 transcription beyond prostate cancer unknown","Does not address PDPK1 protein-level regulation"]},{"year":2024,"claim":"Proposed a tripartite N-MYC-WDR5-PDPK1 complex co-regulating mitotic gene expression, extending PDPK1 into transcriptional/chromatin control.","evidence":"RNA-seq, co-IP for N-MYC-PDPK1 interaction, and comparison with WDR5 inhibition data in neuroblastoma","pmids":["38605297"],"confidence":"Low","gaps":["Single co-IP without reciprocal/structural validation of the complex","No demonstration that PDPK1 kinase activity is required for the gene-regulatory effect"]},{"year":2025,"claim":"Confirmed by reconstitution that PDPK1 is a direct upstream kinase of p70S6K1 and that this activity does not require its PH domain.","evidence":"Baculovirus co-expression with kinase-Glo and AlphaScreen kinase assays and immunoblotting","pmids":["39821712"],"confidence":"Medium","gaps":["No active-site mutagenesis to formally exclude indirect activation","Phosphosite on p70S6K1 not mapped in this assay"]},{"year":2026,"claim":"Identified SENP3 as a direct PDPK1 deSUMOylase at K296 that destabilizes PDPK1 via K48-ubiquitination, linking PDPK1 turnover to suppression of PI3K-AKT signaling in intestinal ischemia/reperfusion.","evidence":"IP-mass spectrometry, co-IP, K296 mutagenesis, ubiquitination assays, and SENP3 knockdown","pmids":["42140449"],"confidence":"Medium","gaps":["E3 ligase mediating the K48-ubiquitination after deSUMOylation not identified","Relationship between K296 and K299 SUMO sites not reconciled"]},{"year":2026,"claim":"Connected PDPK1 to transcriptional anti-apoptotic output via an NFKB1/BIRC3 axis driving radiotherapy resistance.","evidence":"ChIP, dual-luciferase, RNA-seq, siRNA knockdown, and BIRC3 rescue in lung adenocarcinoma","pmids":["41862915"],"confidence":"Medium","gaps":["Whether PDPK1 activates NFKB1 directly or through an intermediate kinase unclear","Single disease context"]},{"year":2026,"claim":"Established PDPK1 as a druggable target in cuproptosis, where kinase inhibition stabilizes the copper transporter CTR1 and promotes copper-dependent cell death.","evidence":"DARTS drug-binding, kinase activity and ubiquitination assays, organoids, and PDX in colorectal cancer (penfluridol)","pmids":["42185682"],"confidence":"Medium","gaps":["How AKT1 phosphorylation controls CTR1 ubiquitination mechanistically not resolved","Penfluridol off-target effects not fully excluded"]},{"year":null,"claim":"The endogenous SUMO E3 ligase and the physiological cues that toggle the K299 SUMOylation / K296 deSUMOylation switch, and how this switch coordinates the bifurcation between mTOR activation and ER-tethered autophagosome biogenesis, remain undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No SUMO E3 ligase identified for PDPK1","Structural basis coupling SUMOylation to S241 autophosphorylation unknown","Reconciliation of K296 versus K299 modification sites needed"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,7,8,18,20]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[1,8,18]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,8,9,18]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4,7,11]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4,6,13]}],"complexes":["PIK3C3(VPS34)-PDPK1 complex","N-MYC-WDR5-PDPK1 complex"],"partners":["AKT1","PIK3C3","SGK3","RPS6KB1","SQSTM1","SENP3","WDR5","RSK2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O15530","full_name":"3-phosphoinositide-dependent protein kinase 1","aliases":[],"length_aa":556,"mass_kda":63.2,"function":"Serine/threonine kinase which acts as a master kinase, phosphorylating and activating a subgroup of the AGC family of protein kinases (PubMed:10226025, PubMed:10480933, PubMed:10995762, PubMed:12167717, PubMed:14585963, PubMed:14604990, PubMed:16207722, PubMed:16251192, PubMed:17327236, PubMed:17371830, PubMed:18835241, PubMed:9094314, PubMed:9368760, PubMed:9445476, PubMed:9445477, PubMed:9707564, PubMed:9768361). Its targets include: protein kinase B (PKB/AKT1, PKB/AKT2, PKB/AKT3), p70 ribosomal protein S6 kinase (RPS6KB1), p90 ribosomal protein S6 kinase (RPS6KA1, RPS6KA2 and RPS6KA3), cyclic AMP-dependent protein kinase (PRKACA), protein kinase C (PRKCD and PRKCZ), serum and glucocorticoid-inducible kinase (SGK1, SGK2 and SGK3), p21-activated kinase-1 (PAK1), TSSK3, protein kinase PKN (PKN1 and PKN2) (PubMed:10226025, PubMed:10480933, PubMed:10995762, PubMed:12167717, PubMed:14585963, PubMed:14604990, PubMed:16207722, PubMed:16251192, PubMed:17327236, PubMed:17371830, PubMed:18835241, PubMed:9094314, PubMed:9368760, PubMed:9445476, PubMed:9707564, PubMed:9768361). Plays a central role in the transduction of signals from insulin by providing the activating phosphorylation to PKB/AKT1, thus propagating the signal to downstream targets controlling cell proliferation and survival, as well as glucose and amino acid uptake and storage (PubMed:10226025, PubMed:12167717, PubMed:9094314). Negatively regulates the TGF-beta-induced signaling by: modulating the association of SMAD3 and SMAD7 with TGF-beta receptor, phosphorylating SMAD2, SMAD3, SMAD4 and SMAD7, preventing the nuclear translocation of SMAD3 and SMAD4 and the translocation of SMAD7 from the nucleus to the cytoplasm in response to TGF-beta (PubMed:17327236). Activates PPARG transcriptional activity and promotes adipocyte differentiation (By similarity). Activates the NF-kappa-B pathway via phosphorylation of IKKB (PubMed:16207722). The tyrosine phosphorylated form is crucial for the regulation of focal adhesions by angiotensin II (PubMed:14585963). Controls proliferation, survival, and growth of developing pancreatic cells (By similarity). Participates in the regulation of Ca(2+) entry and Ca(2+)-activated K(+) channels of mast cells (By similarity). Essential for the motility of vascular endothelial cells (ECs) and is involved in the regulation of their chemotaxis (PubMed:17371830). Plays a critical role in cardiac homeostasis by serving as a dual effector for cell survival and beta-adrenergic response (By similarity). Plays an important role during thymocyte development by regulating the expression of key nutrient receptors on the surface of pre-T cells and mediating Notch-induced cell growth and proliferative responses (By similarity). Provides negative feedback inhibition to toll-like receptor-mediated NF-kappa-B activation in macrophages (By similarity) Catalytically inactive","subcellular_location":"Cytoplasm; Nucleus; Cell membrane; Cell junction, focal adhesion","url":"https://www.uniprot.org/uniprotkb/O15530/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PDPK1","classification":"Common Essential","n_dependent_lines":1076,"n_total_lines":1208,"dependency_fraction":0.890728476821192},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000140992","cell_line_id":"CID001234","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"membrane","grade":1}],"interactors":[{"gene":"PDPK1;PDPK2P","stoichiometry":10.0},{"gene":"CASP3","stoichiometry":0.2},{"gene":"CDSN","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001234","total_profiled":1310},"omim":[{"mim_id":"619443","title":"MEIS 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colorectal cancer cells reduces GSK3β and mTOR activation, whereas AKT1/AKT2 double knockout affects FOXO proteins but not GSK3β or mTOR, placing PDPK1 upstream of GSK3β and mTOR in a pathway distinct from AKT in this context.\",\n      \"method\": \"Targeted homologous recombination knockout in human colon cancer cell lines; downstream signaling assessed by western blot\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic KO with defined downstream signaling readouts, replicated across multiple cell lines, orthogonal to AKT KO results\",\n      \"pmids\": [\"20133737\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PDPK1 phosphorylates and activates RSK2, AKT, c-MYC, IRF4, and cyclin Ds in multiple myeloma cells; PDPK1 inhibition induces apoptosis via activation of BIM and BAD.\",\n      \"method\": \"Pharmacological inhibition and siRNA knockdown of PDPK1 in multiple myeloma cell lines; western blot for downstream substrates and apoptotic markers\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined molecular readouts, single lab, two orthogonal methods (inhibitor + siRNA)\",\n      \"pmids\": [\"25269480\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Chlamydia trachomatis infection activates PDPK1 signaling, which phosphorylates and stabilizes MYC; PDPK1-MYC signaling induces hexokinase II (HKII) expression and HKII translocation/enrichment at mitochondria to prevent apoptosis of infected cells.\",\n      \"method\": \"Biochemical approaches (co-immunoprecipitation, western blot), imaging, pharmacological inhibition of PDPK1 and MYC, exogenous peptides blocking HKII-mitochondria interaction\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biochemical and imaging methods in single lab establishing the PDPK1-MYC-HKII axis\",\n      \"pmids\": [\"28803120\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The MID1 ubiquitin ligase complex associates with PDPK1 mRNA via a purine-rich MIDAS sequence motif, increasing its translational efficiency; PDPK1 protein synthesis is significantly reduced in cells from Opitz syndrome patients with mutated MID1 and can be rescued by functional MID1.\",\n      \"method\": \"mRNA co-immunoprecipitation, translational efficiency assays, patient-derived cell comparison, MID1 rescue experiments\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (co-IP, reporter assay, patient cells, rescue), single lab\",\n      \"pmids\": [\"21930711\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PDPK1 SUMOylation at lysine 299 (within the kinase domain) is required for its autophosphorylation at serine 241 and subsequent activation of AKT1-MTOR signaling; SUMOylation of PDPK1 is inhibited by binding to PIK3C3, and non-SUMOylated PDPK1 tethers LC3 to the ER to initiate autophagosome biogenesis.\",\n      \"method\": \"Co-immunoprecipitation, site-directed mutagenesis (K299), in vivo SUMOylation assays, autophagy detection (LC3 localization), biochemical fractionation\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods including mutagenesis and co-IP, single lab\",\n      \"pmids\": [\"32876514\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Avibirnavirus VP3 CC3 domain disrupts the PIK3C3-PDPK1 complex by directly binding to PIK3C3; release of PDPK1 from PIK3C3 allows PDPK1 to activate the AKT-MTOR pathway, suppressing autophagy to facilitate viral replication.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, autophagy assays, viral replication assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with domain mapping establishing direct interaction, single lab\",\n      \"pmids\": [\"31885313\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"UBC9-mediated SUMOylation of PDPK1 at lysine 299 is required for PDPK1 autophosphorylation at serine 241 and downstream mTORC1 activation; loss of PDPK1 SUMOylation impairs CD4 T-cell glycolytic metabolism and homeostatic proliferation.\",\n      \"method\": \"SUMOylation site mutagenesis (K299), autophosphorylation assays, mTORC1 activity assays, T-cell proliferation and glycolysis assays in vivo and in vitro\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — mutagenesis identifying specific SUMOylation site plus functional readouts, single lab\",\n      \"pmids\": [\"35210408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Coronavirus M protein recruits PDPK1 to phosphorylate SQSTM1 (p62) at threonine 138, directing autophagy substrate selection from virophagy toward mitophagy, thereby suppressing innate immunity and promoting viral replication.\",\n      \"method\": \"Dual split-fluorescence assay, site-directed mutagenesis (T138), co-immunoprecipitation, viral replication assays, PDPK1-targeting peptide inhibition, mouse infection model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — mutagenesis identifying phosphorylation site, multiple orthogonal methods (fluorescence assay, co-IP, peptide inhibitor, in vivo model), single lab with rigorous controls\",\n      \"pmids\": [\"39414765\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PDPK1 mediates prostate cancer cell survival predominantly via phosphorylation and activation of SGK3; PDPK1 knockdown reduces SGK3 phosphorylation, induces apoptosis, and constitutively active SGK3 rescues apoptosis caused by PDPK1 loss, while AKT and SGK1 phosphorylation were not affected.\",\n      \"method\": \"shRNA knockdown, ectopic expression of constitutively active SGK3, western blot for phosphorylation status, apoptosis assays\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis via rescue experiment, two orthogonal approaches (KD + OE), single lab\",\n      \"pmids\": [\"32926495\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Physical interaction between AKT1 and PDPK1 is required for AKT1 activation; a small molecule inhibitor (NSC156529) that specifically disrupts the AKT1-PDPK1 interaction downregulates AKT1 signaling, decreases cancer cell proliferation in vitro, and inhibits prostate tumor xenograft growth in vivo.\",\n      \"method\": \"Live cell-based screen for protein-protein interaction inhibitors, western blot for AKT1 phosphorylation, cell proliferation assays, in vivo xenograft model\",\n      \"journal\": \"Molecular cancer therapeutics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interaction-based mechanism validated with functional readouts in vitro and in vivo, single lab\",\n      \"pmids\": [\"26294745\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ARL15 knockdown specifically inhibits PDPK1 phosphorylation at Ser241, thereby reducing PDPK1 activity and downstream AKT Thr308 phosphorylation in the insulin signaling pathway; ARL15 interacts with ASAP2 (a GAP for ARL15) as identified by co-immunoprecipitation.\",\n      \"method\": \"ARL15 overexpression and knockdown in C2C12 myotubes, western blot for PDPK1-S241 and AKT-T308 phosphorylation, co-immunoprecipitation for ARL15-ASAP2 interaction\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single co-IP and western blot methods without reconstitution or mutagenesis\",\n      \"pmids\": [\"28322786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"AQP3 accumulation (caused by FBXW5 knockdown) induces lysosomal-dependent degradation of PDPK1, thereby inactivating the AKT-MTOR pathway and inducing autophagic cell death in hepatocellular carcinoma cells.\",\n      \"method\": \"FBXW5 knockdown, AQP3 overexpression/knockdown, lysosomal inhibition, western blot for PDPK1 and AKT-MTOR pathway components, autophagy assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple genetic perturbations with defined molecular mechanism, single lab, orthogonal pathway validation\",\n      \"pmids\": [\"38726865\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"LIFR-K620 acetylation facilitates LIFR homodimerization and LIFR-S1044 phosphorylation, which recruits PDPK1 to activate AKT signaling; PDPK1 in turn enhances GCN5 protein level, forming a positive feedback loop sustaining LIFR-K620 acetylation.\",\n      \"method\": \"Liquid mass spectrometry, genetically engineered mouse models, organoid assays, co-immunoprecipitation, lentiviral constructs\",\n      \"journal\": \"Clinical and translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods including mass spectrometry and GEM models, single lab\",\n      \"pmids\": [\"35172032\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"SENP3 directly interacts with PDPK1 (identified by co-immunoprecipitation/mass spectrometry), promotes PDPK1 deSUMOylation at Lys296, leading to increased K48-linked ubiquitination and proteasomal degradation of PDPK1, thereby suppressing PI3K-AKT signaling and inducing apoptosis during intestinal ischemia/reperfusion.\",\n      \"method\": \"Immunoprecipitation-mass spectrometry, co-immunoprecipitation, site-directed mutagenesis (K296), ubiquitination assays, SENP3 knockdown, western blot for PI3K-AKT pathway\",\n      \"journal\": \"Biochemical pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — mutagenesis identifying SUMOylation site, mass spectrometry interaction discovery, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"42140449\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CPT1A mediates succinylation of SP5, which strengthens SP5 binding to the PDPK1 promoter and activates PDPK1 transcription; elevated PDPK1 then activates AKT/mTOR signaling to promote prostate cancer cell viability and glycolysis.\",\n      \"method\": \"Luciferase reporter assay, ChIP assay, co-immunoprecipitation, CCK-8, Seahorse glycolysis assay\",\n      \"journal\": \"Cancer biology & therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and luciferase assays establishing transcriptional mechanism, co-IP for protein interaction, single lab\",\n      \"pmids\": [\"38494680\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"N-MYC physically interacts with PDPK1 through the WDR5-PDPK1 interaction in neuroblastoma cells; PDPK1 and N-MYC co-regulate a specific set of genes involved in spindle pole formation and chromosome segregation, overlapping with WDR5-regulated genes, suggesting a tripartite N-MYC-WDR5-PDPK1 complex regulates mitotic gene expression.\",\n      \"method\": \"RNA-seq transcriptomic analysis, co-immunoprecipitation for N-MYC-PDPK1 physical interaction, comparative analysis with WDR5 inhibition data\",\n      \"journal\": \"BMC genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single co-IP for physical interaction, transcriptomic analysis for gene regulation, single lab, limited functional validation\",\n      \"pmids\": [\"38605297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Vascular endothelial-specific deletion of PDPK1 (Tie2-Cre) reduces islet blood flow, decreases endothelial fenestration, causes hypoxia in islets, and leads to reduced pancreatic beta cell mass and impaired glucose-stimulated insulin secretion, demonstrating a role for endothelial PDPK1 in maintaining islet vascularity and beta cell function.\",\n      \"method\": \"Conditional knockout mice (Tie2+/-/Pdpk1flox/flox), glucose tolerance tests, insulin secretion assays, microsphere islet blood flow measurement, immunohistochemistry, electron microscopy\",\n      \"journal\": \"Diabetologia\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — rigorous conditional KO with multiple orthogonal readouts (functional, histological, molecular), well-controlled mouse model\",\n      \"pmids\": [\"31055616\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PDPK1 activates NFKB1, which transactivates the anti-apoptotic gene BIRC3; BIRC3 overexpression reverses pro-apoptotic effects of PDPK1 knockdown, establishing PDPK1/NFKB1/BIRC3 as a signaling axis driving radiotherapy resistance in lung adenocarcinoma.\",\n      \"method\": \"ChIP assay, dual-luciferase assay, RNA sequencing, siRNA knockdown, BIRC3 overexpression rescue, colony formation and apoptosis assays\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and luciferase establishing direct transcriptional regulation, genetic epistasis via rescue, single lab\",\n      \"pmids\": [\"41862915\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PDPK1 co-expressed with RPS6KB1 (p70S6K1) in a baculovirus system phosphorylates and activates p70S6K1, confirming PDPK1 as a direct upstream kinase of p70S6K1; a PH-domain-deleted PDPK1 construct was sufficient for this activity.\",\n      \"method\": \"Baculovirus dual expression system, Kinase-Glo assay, AlphaScreen kinase assay, immunoblotting\",\n      \"journal\": \"Molecular biology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro reconstitution of kinase activity with validated assays, single lab, no mutagenesis of active site\",\n      \"pmids\": [\"39821712\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In small-cell lung cancer cells, PDPK1 and Akt affect Hedgehog pathway expression (PDPK1 silencing reduces Hedgehog expression), but Hedgehog does not affect PDPK1 or p-Akt expression, placing PDPK1-Akt upstream of Hedgehog signaling.\",\n      \"method\": \"siRNA transfection for PDPK1 and Akt silencing, pharmacological Hedgehog inhibition, proliferation and migration assays, western blot\",\n      \"journal\": \"The Journal of international medical research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — genetic epistasis by single-gene knockdown, single lab, no reconstitution or direct interaction data\",\n      \"pmids\": [\"34038205\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PDPK1 directly binds penfluridol (demonstrated by drug affinity responsive target stability assay); penfluridol inhibits PDPK1 kinase activity and reduces AKT1 phosphorylation, which decreases CTR1 ubiquitination, stabilizes CTR1 on the plasma membrane, and promotes intracellular copper accumulation leading to cuproptosis in colorectal cancer.\",\n      \"method\": \"Drug affinity responsive target stability (DARTS) assay, PDPK1 kinase activity assay, ubiquitination assay, western blot for p-AKT1 and CTR1, patient-derived organoids, PDX model\",\n      \"journal\": \"Acta pharmacologica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct drug-target binding confirmed by DARTS, kinase activity measured, multiple model systems, single lab\",\n      \"pmids\": [\"42185682\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PDPK1 is a serine/threonine kinase that occupies a central node in PI3K signaling: it directly phosphorylates and activates multiple AGC-family kinases (AKT at T308, SGK3, RSK2, S6K/p70S6K1) to regulate cell survival, growth, glycolysis, and autophagy; its activity is governed by post-translational modifications including SUMOylation at K299 (required for autophosphorylation at S241 and mTORC1 activation) and deSUMOylation by SENP3 at K296 (which triggers K48-ubiquitination and proteasomal degradation); it forms regulated complexes with PIK3C3 (VPS34), AKT1, and WDR5/N-MYC that control autophagosome biogenesis and mitotic gene expression; it phosphorylates SQSTM1-T138 to direct autophagy cargo selection; and in endothelial cells it maintains pancreatic islet vascularity and beta cell function in vivo.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PDPK1 is a serine/threonine kinase that occupies a central node in PI3K-AKT/mTOR signaling, transducing growth, survival, and metabolic cues by directly phosphorylating and activating multiple AGC-family kinases [#1, #8, #18]. It activates AKT through a required physical interaction, and disrupting the AKT1-PDPK1 interface with a small molecule downregulates AKT signaling and tumor growth [#9]; in distinct cellular contexts it selectively routes survival signaling through SGK3 in prostate cancer [#8], through RSK2, c-MYC, IRF4, and cyclin Ds in multiple myeloma [#1], and directly phosphorylates p70S6K1 in vitro [#18]. Genetically, PDPK1 lies upstream of GSK3\\u03b2 and mTOR in a branch distinct from AKT-FOXO signaling [#0]. PDPK1 activity is gated by SUMOylation at K299 by UBC9, which is required for its S241 autophosphorylation and downstream mTORC1 activation, supporting glycolytic metabolism and T-cell proliferation [#6, #4]; deSUMOylation at K296 by SENP3 triggers K48-ubiquitination and proteasomal degradation, suppressing PI3K-AKT signaling [#13]. PDPK1 also controls autophagy: binding to PIK3C3 (VPS34) inhibits its SUMOylation, and non-SUMOylated PDPK1 tethers LC3 to the ER to initiate autophagosome biogenesis [#4], while PDPK1 phosphorylation of SQSTM1/p62 at T138 directs autophagy cargo selection \\u2014 a mechanism hijacked by coronavirus M protein to shift virophagy toward mitophagy and suppress innate immunity [#7]. In vivo, vascular endothelial-specific deletion of PDPK1 reduces islet blood flow and beta cell mass and impairs glucose-stimulated insulin secretion [#16].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established that PDPK1 sits upstream of GSK3\\u03b2 and mTOR in a signaling branch genetically separable from AKT, refining its position in the PI3K pathway.\",\n      \"evidence\": \"Targeted homologous-recombination knockout in human colon cancer lines with downstream signaling readouts, compared against AKT1/AKT2 double knockout\",\n      \"pmids\": [\"20133737\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not identify the direct AKT-independent substrate linking PDPK1 to GSK3\\u03b2/mTOR\", \"Context restricted to colorectal cancer cells\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showed PDPK1 expression is translationally regulated, linking its protein synthesis to the MID1 ubiquitin ligase complex and Opitz syndrome.\",\n      \"evidence\": \"mRNA co-immunoprecipitation, translational efficiency assays, patient-derived cells, and MID1 rescue\",\n      \"pmids\": [\"21930711\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"MIDAS motif binding mechanism on PDPK1 mRNA not structurally defined\", \"Does not establish kinase-pathway consequences of altered PDPK1 levels in patients\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrated PDPK1 drives survival in multiple myeloma by activating a broad set of substrates (RSK2, AKT, c-MYC, IRF4, cyclin Ds), positioning it as a pro-survival therapeutic node.\",\n      \"evidence\": \"Pharmacological inhibition plus siRNA knockdown with apoptotic and substrate readouts\",\n      \"pmids\": [\"25269480\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which substrate phosphorylations are direct versus indirect not resolved\", \"Single disease context\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined the AKT1-PDPK1 physical interaction as required for AKT1 activation and druggable, establishing protein-protein interaction disruption as an anti-tumor strategy.\",\n      \"evidence\": \"Live-cell PPI inhibitor screen (NSC156529), phospho-AKT westerns, proliferation and xenograft assays\",\n      \"pmids\": [\"26294745\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interaction interface not structurally mapped\", \"Inhibitor specificity beyond the AKT1-PDPK1 interface not fully excluded\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Linked PDPK1 to pathogen-driven metabolic rewiring, showing a PDPK1-MYC-HKII axis prevents apoptosis of Chlamydia-infected cells.\",\n      \"evidence\": \"Co-IP, imaging, pharmacological inhibition, and HKII-mitochondria blocking peptides in infected cells\",\n      \"pmids\": [\"28803120\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PDPK1 phosphorylates MYC directly not established\", \"Upstream activator of PDPK1 during infection unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed PDPK1's autophagy-regulatory role and its control by VPS34 binding, with a viral protein exploiting the PIK3C3-PDPK1 complex to suppress autophagy.\",\n      \"evidence\": \"Reciprocal co-IP with domain mapping of avibirnavirus VP3, plus autophagy and viral replication assays\",\n      \"pmids\": [\"31885313\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct PIK3C3-PDPK1 binding interface on PDPK1 not mapped\", \"Endogenous (non-viral) regulator of complex dissociation unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Provided in vivo evidence that endothelial PDPK1 maintains pancreatic islet vascularity and beta cell function, extending PDPK1 biology to organismal metabolic physiology.\",\n      \"evidence\": \"Tie2-Cre conditional knockout mice with glucose tolerance, insulin secretion, islet blood flow, IHC, and EM\",\n      \"pmids\": [\"31055616\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endothelial substrate of PDPK1 mediating fenestration not identified\", \"Cell-autonomous beta cell role not addressed by this model\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified SUMOylation at K299 as a switch governing PDPK1 autophosphorylation and bifurcating its output between mTOR activation and ER-tethered autophagosome initiation.\",\n      \"evidence\": \"K299 mutagenesis, in vivo SUMOylation assays, co-IP with PIK3C3, and LC3 localization/fractionation\",\n      \"pmids\": [\"32876514\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"SUMO ligase responsible not identified in this study\", \"Structural basis of how K299 SUMOylation enables S241 autophosphorylation unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Established SGK3, rather than AKT, as the dominant PDPK1 effector for survival in prostate cancer, demonstrating context-specific substrate selection.\",\n      \"evidence\": \"shRNA knockdown with constitutively active SGK3 rescue and apoptosis readouts\",\n      \"pmids\": [\"32926495\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"What determines SGK3 versus AKT preference in this context not defined\", \"Single cancer type\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Assigned the SUMO E2 UBC9 to PDPK1 K299 SUMOylation and connected this modification to immune-cell glycolysis and homeostatic proliferation.\",\n      \"evidence\": \"K299 mutagenesis, autophosphorylation and mTORC1 assays, and CD4 T-cell proliferation/glycolysis in vivo and in vitro\",\n      \"pmids\": [\"35210408\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 SUMO ligase still not defined\", \"Physiological signal triggering UBC9-PDPK1 SUMOylation unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Placed PDPK1 in a positive feedback loop with LIFR signaling, where LIFR-S1044 phosphorylation recruits PDPK1 to activate AKT and PDPK1 reinforces LIFR acetylation via GCN5.\",\n      \"evidence\": \"Mass spectrometry, co-IP, GEM models, and organoids\",\n      \"pmids\": [\"35172032\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which PDPK1 raises GCN5 levels unclear\", \"Direct PDPK1 substrate in the loop not pinpointed\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed PDPK1 directs autophagy cargo selection by phosphorylating SQSTM1/p62 at T138, a step coronavirus M protein hijacks to switch virophagy to mitophagy and evade innate immunity.\",\n      \"evidence\": \"Dual split-fluorescence, T138 mutagenesis, co-IP, peptide inhibitor, and mouse infection model\",\n      \"pmids\": [\"39414765\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How T138 phosphorylation mechanistically biases cargo recognition not fully resolved\", \"Endogenous (non-viral) signals recruiting PDPK1 to p62 unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated lysosomal-dependent degradation of PDPK1 as a tumor-suppressive route, with AQP3 accumulation inactivating AKT-mTOR and triggering autophagic cell death.\",\n      \"evidence\": \"FBXW5 knockdown, AQP3 modulation, lysosomal inhibition, and AKT-mTOR/autophagy readouts in HCC cells\",\n      \"pmids\": [\"38726865\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between AQP3 and PDPK1 degradation not defined\", \"Whether AQP3 binds PDPK1 directly unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed PDPK1 transcription is driven by SP5, itself controlled by CPT1A-mediated succinylation, connecting metabolic enzyme activity to PDPK1-AKT/mTOR-driven glycolysis.\",\n      \"evidence\": \"Luciferase reporter, ChIP, co-IP, and Seahorse glycolysis assays in prostate cancer cells\",\n      \"pmids\": [\"38494680\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Generality of SP5-driven PDPK1 transcription beyond prostate cancer unknown\", \"Does not address PDPK1 protein-level regulation\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Proposed a tripartite N-MYC-WDR5-PDPK1 complex co-regulating mitotic gene expression, extending PDPK1 into transcriptional/chromatin control.\",\n      \"evidence\": \"RNA-seq, co-IP for N-MYC-PDPK1 interaction, and comparison with WDR5 inhibition data in neuroblastoma\",\n      \"pmids\": [\"38605297\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single co-IP without reciprocal/structural validation of the complex\", \"No demonstration that PDPK1 kinase activity is required for the gene-regulatory effect\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Confirmed by reconstitution that PDPK1 is a direct upstream kinase of p70S6K1 and that this activity does not require its PH domain.\",\n      \"evidence\": \"Baculovirus co-expression with kinase-Glo and AlphaScreen kinase assays and immunoblotting\",\n      \"pmids\": [\"39821712\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No active-site mutagenesis to formally exclude indirect activation\", \"Phosphosite on p70S6K1 not mapped in this assay\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified SENP3 as a direct PDPK1 deSUMOylase at K296 that destabilizes PDPK1 via K48-ubiquitination, linking PDPK1 turnover to suppression of PI3K-AKT signaling in intestinal ischemia/reperfusion.\",\n      \"evidence\": \"IP-mass spectrometry, co-IP, K296 mutagenesis, ubiquitination assays, and SENP3 knockdown\",\n      \"pmids\": [\"42140449\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase mediating the K48-ubiquitination after deSUMOylation not identified\", \"Relationship between K296 and K299 SUMO sites not reconciled\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Connected PDPK1 to transcriptional anti-apoptotic output via an NFKB1/BIRC3 axis driving radiotherapy resistance.\",\n      \"evidence\": \"ChIP, dual-luciferase, RNA-seq, siRNA knockdown, and BIRC3 rescue in lung adenocarcinoma\",\n      \"pmids\": [\"41862915\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PDPK1 activates NFKB1 directly or through an intermediate kinase unclear\", \"Single disease context\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Established PDPK1 as a druggable target in cuproptosis, where kinase inhibition stabilizes the copper transporter CTR1 and promotes copper-dependent cell death.\",\n      \"evidence\": \"DARTS drug-binding, kinase activity and ubiquitination assays, organoids, and PDX in colorectal cancer (penfluridol)\",\n      \"pmids\": [\"42185682\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How AKT1 phosphorylation controls CTR1 ubiquitination mechanistically not resolved\", \"Penfluridol off-target effects not fully excluded\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The endogenous SUMO E3 ligase and the physiological cues that toggle the K299 SUMOylation / K296 deSUMOylation switch, and how this switch coordinates the bifurcation between mTOR activation and ER-tethered autophagosome biogenesis, remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No SUMO E3 ligase identified for PDPK1\", \"Structural basis coupling SUMOylation to S241 autophosphorylation unknown\", \"Reconciliation of K296 versus K299 modification sites needed\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 7, 8, 18, 20]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [1, 8, 18]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 8, 9, 18]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4, 7, 11]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4, 6, 13]}\n    ],\n    \"complexes\": [\n      \"PIK3C3(VPS34)-PDPK1 complex\",\n      \"N-MYC-WDR5-PDPK1 complex\"\n    ],\n    \"partners\": [\n      \"AKT1\",\n      \"PIK3C3\",\n      \"SGK3\",\n      \"RPS6KB1\",\n      \"SQSTM1\",\n      \"SENP3\",\n      \"WDR5\",\n      \"RSK2\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}