{"gene":"PRKD3","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2008,"finding":"PKD3 promotes prostate cancer cell growth and survival through a PKCε/PKD3 pathway downstream of Akt and ERK1/2. PKCε regulates PKD3 kinase activity and nuclear localization in PC3 and DU145 cells. Overexpression of PKD3 blocks PMA-induced apoptosis, prolonged ERK1/2 activation, and promotes S phase entry; depletion causes G0-G1 arrest. PKD3-mediated Akt upregulation requires PI3K and p38.","method":"Overexpression and siRNA knockdown of PKD3, cell cycle analysis, kinase activity assays, Western blotting for Akt and ERK1/2, immunohistochemistry for subcellular localization","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (KD/OE, cell cycle, kinase activity), single lab","pmids":["18483269"],"is_preprint":false},{"year":2012,"finding":"PKD3 promotes prostate cancer cell invasion by phosphorylating Ser536 on p65 NF-κB, thereby activating uPA transcription. PKD3 also interacts with and suppresses HDAC1, reducing HDAC1 binding to the uPA promoter and thus de-repressing uPA expression. PKD3 interacts physically with IKKβ.","method":"siRNA knockdown of PKD2/PKD3, Co-IP (PKD3–IKKβ and PKD3–HDAC1 interactions), ChIP for p65 binding to uPA promoter, rescue experiments with constitutive Ser536 p65 and p65 overexpression, invasion/migration assays","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, ChIP, epistatic rescue experiments, multiple orthogonal methods in single lab","pmids":["22797919"],"is_preprint":false},{"year":2021,"finding":"TRIM47 forms a ternary complex with PKCε and PKD3, stabilizing both kinases. TRIM47 promotes lysine-27-linked polyubiquitination of PKCε, and this complex activates NF-κB signaling to drive breast cancer proliferation and endocrine therapy resistance.","method":"Co-immunoprecipitation (TRIM47–PKCε–PKD3 complex), ubiquitination assays, overexpression and siRNA knockdown in MCF-7 and OHTR cells, proliferation assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ubiquitination assays, single lab, two orthogonal methods","pmids":["34433666"],"is_preprint":false},{"year":2013,"finding":"PKD3 activates S6K1 (a downstream target of mTORC1) in triple-negative breast cancer cells. PKD3 knockdown reduces S6K1 phosphorylation, impairs mTORC1 activation at endolysosomal membranes, causes accumulation of mannose-6-phosphate receptor, and recruits the autophagy marker LC3 to enlarged acidic vesicles.","method":"Antibody array, siRNA knockdown, Western blotting for S6K1 phosphorylation, immunofluorescence for endolysosomal markers and LC3","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — antibody array plus mechanistic follow-up with KD and imaging, single lab","pmids":["24337579"],"is_preprint":false},{"year":2012,"finding":"PKD3 directly phosphorylates GIT1 on serine 46. This phosphorylation acts as a molecular switch that shifts GIT1 localization from focal adhesions to motile, paxillin-positive cytoplasmic complexes, thereby regulating paxillin trafficking and cellular protrusive activity.","method":"Mass spectrometry-based phosphoproteomics to identify GIT1 S46 as PKD3 substrate, siRNA knockdown of PKD3, phosphomimetic (S46D) and phospho-deficient (S46A) GIT1 mutants, immunofluorescence imaging of GIT1 localization and paxillin","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct substrate identification by MS, mutagenesis-based functional validation, mechanistic imaging readout","pmids":["22893698"],"is_preprint":false},{"year":2019,"finding":"PKD3 is the predominant PKD isoform in hepatocytes and provides negative feedback on insulin signaling by suppressing AKT, mTORC1, and mTORC2 activity. Hepatic deletion of PKD3 in mice improves insulin-induced glucose tolerance but increases SREBP-mediated lipogenesis and hepatic triglyceride/cholesterol content on a high-fat diet. Constitutively active PKD3 overexpression causes insulin resistance.","method":"Hepatic-specific PKD3 knockout mouse, constitutively active PKD3 overexpression mouse model, glucose tolerance tests, Western blotting for AKT/mTORC1/mTORC2, SREBP pathway analysis, lipid measurements","journal":"Science signaling","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo genetic loss-of-function and gain-of-function mouse models, multiple orthogonal metabolic readouts, replicated across conditions","pmids":["31387939"],"is_preprint":false},{"year":2019,"finding":"PKD3 interacts with SREBP1 in prostate cancer cells, promotes maturation of SREBP1 (68 kDa form), and enhances SREBP1 binding to the FASN promoter to upregulate de novo lipogenesis. PKD3 silencing reduces lipid content and expression of FASN and ACLY; overexpression of SREBP1 rescues the growth suppression caused by PKD3 depletion.","method":"Co-immunoprecipitation (PKD3–SREBP1), ChIP (SREBP1 at FASN promoter), siRNA knockdown, SREBP1 overexpression rescue, lipid content assays, Western blotting","journal":"Journal of Cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ChIP, epistatic rescue, single lab","pmids":["31772672"],"is_preprint":false},{"year":2008,"finding":"PKD3 is the predominant PKD isoform in mouse exocrine pancreatic acinar cells. It undergoes rapid membrane translocation, trans-activating phosphorylation, and kinase activation after gastrointestinal hormone or cholinergic stimulation via a Ca2+-independent, diacylglycerol- and PKC-dependent mechanism. PKD3 activation potentiates MEK/ERK/RSK signaling and enhances cholecystokinin-mediated amylase secretion.","method":"Differential PKD isoform expression analysis, membrane fractionation/translocation assays, pharmacological PKC inhibition, ERK/RSK Western blotting, amylase secretion assay in isolated acinar cells","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods in isolated primary acinar cells, single lab","pmids":["19028687"],"is_preprint":false},{"year":2005,"finding":"The C1a domain of PKD3 is responsible for high-affinity phorbol ester ([3H]PDBu) binding, while C1b has no detectable binding activity. Both C1a and PKD3 kinase activity are required for phorbol ester (PMA)-induced plasma membrane translocation of PKD3. PKC, by directly activating PKD3, regulates its plasma membrane localization.","method":"Radioligand binding assay ([3H]PDBu), C1a/C1b point mutations, GFP-tagged PKD3 live-cell imaging, constitutively active and kinase-dead PKD3 constructs, PKC inhibitor RO 31-8220","journal":"Cellular signalling","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro binding assay with mutagenesis, live-cell translocation imaging, pharmacological validation, multiple orthogonal approaches","pmids":["15927450"],"is_preprint":false},{"year":2010,"finding":"PKD3 co-localizes with the androgen receptor (AR) in the nucleus of LNCaP cells after DHT stimulation. Wild-type PKD3 significantly increases AR transcriptional activity and PSA expression in response to DHT; kinase-dead PKD3 partially reduces AR transcriptional activity, indicating kinase activity is required.","method":"Dual-luciferase AR reporter assay, RT-QPCR for PSA mRNA, confocal microscopy for PKD3/AR co-localization, overexpression of wild-type vs. kinase-dead PKD3","journal":"Nan fang yi ke da xue xue bao (Journal of Southern Medical University)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reporter assay, co-localization imaging, kinase-dead mutant, single lab","pmids":["20813663"],"is_preprint":false},{"year":2016,"finding":"PKD3 deficiency in mouse embryonic fibroblasts impairs microtubule nucleation and dynamics during the cell cycle. PKD1 can partially compensate for PKD3 function in this process.","method":"Genetic PKD3 knockout MEFs, microtubule nucleation and dynamics assays, cell cycle analysis","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO model with specific cellular phenotype, single lab","pmids":["27245420"],"is_preprint":false},{"year":2016,"finding":"PKD2 and PKD3 are activated in cardiomyocytes and cardiac fibroblasts by sphingosine-1-phosphate, thrombin, PDGF, and H2O2 via PKC-dependent pathways. A novel role for Rho was identified in sphingosine-1-phosphate and thrombin receptor-dependent activation of PKD2/3 and downstream CREB phosphorylation in cardiomyocytes.","method":"Phos-tag SDS-PAGE, PKC inhibitor GF109203X, Rho inhibitor C3 toxin, CREB phosphorylation assays, in isolated cardiac fibroblasts and cardiomyocytes","journal":"Journal of molecular and cellular cardiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Phos-tag SDS-PAGE with pharmacological epistasis, single lab, two cell types","pmids":["27515283"],"is_preprint":false},{"year":2010,"finding":"PKD1 and PKD3 are both activated by orexin-A (via orexin receptor 1) and translocate to the plasma membrane. Overexpression of kinase-dead PKD1 or kinase-dead PKD3 disrupts orexin-A-induced calcium oscillations, demonstrating a functional role for PKD3 kinase activity in modulating Ca2+ responses.","method":"Phosphospecific antibody detection of PKD1/PKD3 activation, dominant-negative (kinase-dead) PKD1 and PKD3 overexpression, intracellular calcium imaging in HEKOx1R cells","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — kinase-dead dominant negative approach with calcium imaging readout, single lab","pmids":["20621130"],"is_preprint":false},{"year":2019,"finding":"The RhoGEF GEF-H1 acts upstream of PKD3 activation in triple-negative breast cancer stem cells. PKD3 is required for maintenance of the TNBC stem cell population, as its depletion reduces cancer stem cell frequency in vitro and tumor initiation potential in vivo.","method":"PKD3 siRNA knockdown, in vitro oncosphere and colony formation assays, in vivo tumor initiation assay, pharmacological PKD inhibition combined with paclitaxel","journal":"International journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KD with in vitro and in vivo functional readouts plus pharmacological validation, single lab","pmids":["31745977"],"is_preprint":false},{"year":2021,"finding":"PKD3 activates PKA and regulates PKA-mediated glucose and tyrosine metabolism in hepatocytes. PKD3 is activated by glucagon and promotes glucose and tyrosine levels in hepatocytes. Identified >300 putative PKD3 substrates by phosphoproteomics, including phenylalanine hydroxylase (PAH) as a downstream PKA target.","method":"Phosphoproteomics on PKD3-deficient hepatocytes, biochemical PKA activity assays, glucagon stimulation, glucose and tyrosine metabolite measurements","journal":"Life science alliance","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phosphoproteomics plus biochemical validation, single lab","pmids":["34145024"],"is_preprint":false},{"year":2023,"finding":"Hsp90 physically interacts with PKD3 to ensure its conformational stability. Pharmacological Hsp90 inhibition causes proteasomal degradation of PKD3 and abrogates PKD3-dependent prostate cancer cell migration. PKD3 is thus an Hsp90 client protein.","method":"Proximity ligation assay, co-immunoprecipitation (Hsp90–PKD3), Hsp90 inhibitor (ganetespib) treatment, proteasome inhibition rescue, PKD3 siRNA combined with ganetespib, ectopic PKD3 overexpression in LNCaP cells","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus PLA plus functional rescue, single lab","pmids":["36672148"],"is_preprint":false},{"year":2026,"finding":"PRKCN (PKD3) physically interacts with mTOR and activates mTORC1/C2 signaling to sustain IRF4 expression in multiple myeloma. PRKCN and IRF4 form a feed-forward transcriptional circuit: IRF4 directly induces PRKCN transcription, and PRKCN fosters IRF4 expression via mTOR. This function is independent of PKD3 kinase activity but requires activation-loop phosphorylation.","method":"Co-immunoprecipitation (PRKCN–mTOR), constitutive/inducible knockdown, kinase-dead mutant analysis, ChIP-seq/luciferase for IRF4-PRKCN circuit, in vivo xenograft models, pharmacological PRKCN inhibitor","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, kinase-dead mutant, in vivo xenograft validation, single lab with multiple orthogonal methods","pmids":["41655233"],"is_preprint":false},{"year":2025,"finding":"Endogenous PKD3 localizes to Rab7-positive late endosomes in MDA-MB-231 TNBC cells cultured on stiff matrices. PKD3 depletion results in smaller Rab7-positive vesicles, reduced retromer complex recruitment, enhanced cathepsin D secretion, impaired endosomal acidification, dysregulated Wnt signaling, and a decline in cancer stemness.","method":"Endogenous PKD3 localization by immunofluorescence, siRNA PKD3 knockdown, Rab7 vesicle size quantification, retromer recruitment assay, cathepsin D secretion assay, endosomal pH measurement, Wnt signaling and stemness assays","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment tied to functional consequence with multiple orthogonal readouts, single lab","pmids":["40970203"],"is_preprint":false}],"current_model":"PRKD3 (PKD3) is a DAG/phorbol ester-activated serine-threonine kinase whose C1a domain mediates membrane recruitment; it is activated downstream of PKC (and Rho in some contexts) and operates at multiple subcellular compartments—plasma membrane, Golgi, nucleus, and Rab7-positive late endosomes—where it phosphorylates substrates including GIT1-S46 (regulating focal adhesion dynamics), p65 NF-κB-S536 (promoting uPA transcription and invasion), and interacts with SREBP1, HDAC1, IKKβ, mTOR, and Hsp90 to coordinate cell proliferation, survival, lipogenesis, insulin feedback, endolysosomal homeostasis, and cancer stem cell maintenance."},"narrative":{"mechanistic_narrative":"PRKD3 (PKD3) is a diacylglycerol/phorbol ester-responsive serine-threonine kinase that acts as a downstream effector of protein kinase C to couple receptor and lipid signaling to proliferation, survival, metabolism, and invasion across multiple tissues [PMID:18483269, PMID:19028687, PMID:15927450]. Its C1a domain mediates high-affinity phorbol ester binding, and both C1a and intrinsic kinase activity are required for PMA-induced plasma-membrane translocation, with PKC directly activating PKD3 to control its localization [PMID:15927450]; activation downstream of PKC (and, in cardiomyocytes, Rho) is broadly elicited by hormonal, cholinergic, and growth-factor stimuli [PMID:19028687, PMID:27515283, PMID:20621130]. Once activated, PKD3 drives a pro-invasive transcriptional program by phosphorylating p65 NF-κB on Ser536 and suppressing HDAC1 to de-repress uPA, and it directly phosphorylates GIT1 on Ser46 to shift GIT1 between focal adhesions and motile paxillin-positive complexes, linking the kinase to focal-adhesion dynamics and cell motility [PMID:22797919, PMID:22893698]. PKD3 also governs lipid and glucose metabolism: it interacts with SREBP1 to promote its maturation and FASN-driven lipogenesis in prostate cancer, and in hepatocytes it is the predominant isoform, exerting negative feedback on AKT/mTORC1/mTORC2 insulin signaling while activating PKA-mediated glucose and tyrosine metabolism [PMID:31387939, PMID:31772672, PMID:34145024]. In cancer, PKD3 supports mTORC1/mTORC2 signaling at endolysosomal membranes, localizes to Rab7-positive late endosomes to sustain retromer recruitment and endosomal acidification, and maintains triple-negative breast cancer and multiple myeloma stem/tumor-initiating populations, in part through an IRF4 feed-forward circuit and Hsp90-dependent stabilization [PMID:24337579, PMID:31745977, PMID:36672148, PMID:41655233, PMID:40970203].","teleology":[{"year":2005,"claim":"Established the structural basis for PKD3 membrane recruitment, answering how the kinase senses lipid second messengers and is positioned at the plasma membrane.","evidence":"Radioligand binding with C1a/C1b mutants and live-cell imaging of GFP-PKD3 with PKC inhibition","pmids":["15927450"],"confidence":"High","gaps":["Does not define which substrates are phosphorylated at the membrane","Structural model of the activated kinase not resolved"]},{"year":2008,"claim":"Defined PKD3 as a pro-growth, pro-survival effector in a PKCε/PKD3 axis, framing its role in cell-cycle progression and apoptosis resistance.","evidence":"Overexpression/siRNA in prostate cancer cells with cell-cycle, kinase-activity, and ERK/Akt readouts","pmids":["18483269","19028687"],"confidence":"Medium","gaps":["Direct nuclear substrates not identified","Mechanism of nuclear localization control unresolved"]},{"year":2012,"claim":"Identified two direct mechanistic outputs of PKD3 — transcriptional de-repression of uPA via p65/HDAC1 and a direct GIT1-S46 phosphorylation switch — connecting the kinase to invasion and focal-adhesion dynamics.","evidence":"Reciprocal Co-IP, ChIP, epistatic rescue, and MS-based substrate identification with phosphomimetic mutants","pmids":["22797919","22893698"],"confidence":"High","gaps":["Whether p65-S536 is a direct PKD3 substrate vs. indirect not fully separated","GIT1-S46 switch not validated in vivo"]},{"year":2013,"claim":"Placed PKD3 upstream of mTORC1 at endolysosomal membranes, linking it to autophagy and lysosomal homeostasis in TNBC.","evidence":"Antibody array, siRNA knockdown, and immunofluorescence for endolysosomal/LC3 markers","pmids":["24337579"],"confidence":"Medium","gaps":["Direct mTORC1-pathway substrate of PKD3 not identified","Mechanism of endolysosomal recruitment unresolved"]},{"year":2019,"claim":"Revealed PKD3 as a tissue-specific metabolic regulator and a lipogenesis driver, showing context-dependent suppression of insulin signaling in liver versus SREBP1-driven lipogenesis in cancer.","evidence":"Hepatic knockout/constitutively-active mouse models with metabolic readouts, and Co-IP/ChIP/rescue for SREBP1-FASN in prostate cancer","pmids":["31387939","31772672","31745977"],"confidence":"High","gaps":["Direct PKD3 phosphorylation sites on insulin-pathway components not mapped","Reconciliation of pro- vs anti-mTOR roles across tissues incomplete"]},{"year":2021,"claim":"Expanded PKD3 regulatory inputs and outputs, identifying TRIM47-mediated kinase stabilization and a glucagon/PKA metabolic branch with a large putative substrate set.","evidence":"Co-IP, ubiquitination assays in breast cancer cells, and phosphoproteomics with PKA biochemical validation in hepatocytes","pmids":["34433666","34145024"],"confidence":"Medium","gaps":["Most of the >300 putative substrates not individually validated","Direct vs PKA-mediated phosphorylation events not distinguished"]},{"year":2023,"claim":"Established PKD3 as an Hsp90 client whose stability is chaperone-dependent, identifying a druggable vulnerability for PKD3-driven migration.","evidence":"PLA, reciprocal Co-IP, Hsp90 inhibition with proteasome-rescue in prostate cancer cells","pmids":["36672148"],"confidence":"Medium","gaps":["Hsp90 co-chaperone requirements not defined","Effect on other PKD3 functions beyond migration untested"]},{"year":2025,"claim":"Resolved an endosomal function for endogenous PKD3 at Rab7-positive late endosomes governing retromer recruitment, acidification, and stemness, anchoring earlier endolysosomal phenotypes to a defined compartment.","evidence":"Endogenous immunofluorescence localization plus retromer, cathepsin D secretion, endosomal pH, and Wnt/stemness assays in TNBC","pmids":["40970203"],"confidence":"Medium","gaps":["Endosomal PKD3 substrates not identified","Mechanism coupling PKD3 to retromer recruitment unknown"]},{"year":2026,"claim":"Defined a kinase-activity-independent scaffolding role for PKD3 in an mTOR/IRF4 feed-forward circuit sustaining multiple myeloma, showing PKD3 functions extend beyond catalysis.","evidence":"Co-IP with mTOR, kinase-dead mutant analysis, ChIP-seq/luciferase, and xenograft models","pmids":["41655233"],"confidence":"Medium","gaps":["How activation-loop phosphorylation enables kinase-independent function unclear","Direct PKD3-mTOR binding interface not mapped"]},{"year":null,"claim":"The unifying logic that determines which PKD3 outputs (transcriptional, metabolic, endosomal, scaffolding) dominate in a given cell type, and the full direct substrate repertoire, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No comprehensive validated direct substrate map","Context-dependent compartment selection mechanism unknown","No structural model of activated full-length PKD3"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,4]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[4,8]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[8]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,9,16]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[8,12]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,9]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[3,17]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,7,11]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[5,6,14]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,9,16]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[13,16,17]}],"complexes":["TRIM47-PKCε-PKD3 complex"],"partners":["IKKΒ","HDAC1","SREBP1","TRIM47","PKCΕ","HSP90","MTOR","GIT1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O94806","full_name":"Serine/threonine-protein kinase D3","aliases":["Protein kinase C nu type","Protein kinase EPK2","nPKC-nu"],"length_aa":890,"mass_kda":100.5,"function":"Converts transient diacylglycerol (DAG) signals into prolonged physiological effects, downstream of PKC. Involved in resistance to oxidative stress (By similarity)","subcellular_location":"Cytoplasm; Membrane","url":"https://www.uniprot.org/uniprotkb/O94806/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PRKD3","classification":"Not Classified","n_dependent_lines":7,"n_total_lines":1208,"dependency_fraction":0.005794701986754967},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000115825","cell_line_id":"CID001887","localizations":[{"compartment":"big_aggregates","grade":3},{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":2}],"interactors":[{"gene":"PRKD2","stoichiometry":10.0},{"gene":"PRKD1","stoichiometry":4.0},{"gene":"HDAC2","stoichiometry":0.2},{"gene":"RAN","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001887","total_profiled":1310},"omim":[{"mim_id":"607077","title":"PROTEIN KINASE D3; PRKD3","url":"https://www.omim.org/entry/607077"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Vesicles","reliability":"Additional"},{"location":"Basal body","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PRKD3"},"hgnc":{"alias_symbol":["PKD3","EPK2"],"prev_symbol":["PRKCN"]},"alphafold":{"accession":"O94806","domains":[{"cath_id":"3.10.20.90","chopping":"59-149","consensus_level":"high","plddt":83.1645,"start":59,"end":149},{"cath_id":"2.30.29.30","chopping":"418-474_481-499","consensus_level":"high","plddt":86.9983,"start":418,"end":499},{"cath_id":"3.30.200.20","chopping":"563-654","consensus_level":"medium","plddt":78.2435,"start":563,"end":654},{"cath_id":"1.10.510.10","chopping":"657-885","consensus_level":"medium","plddt":84.7709,"start":657,"end":885}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O94806","model_url":"https://alphafold.ebi.ac.uk/files/AF-O94806-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O94806-F1-predicted_aligned_error_v6.png","plddt_mean":68.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PRKD3","jax_strain_url":"https://www.jax.org/strain/search?query=PRKD3"},"sequence":{"accession":"O94806","fasta_url":"https://rest.uniprot.org/uniprotkb/O94806.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O94806/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O94806"}},"corpus_meta":[{"pmid":"18483269","id":"PMC_18483269","title":"Protein kinase D3 (PKD3) contributes to prostate cancer cell growth and survival through a PKCepsilon/PKD3 pathway downstream of Akt and ERK 1/2.","date":"2008","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/18483269","citation_count":111,"is_preprint":false},{"pmid":"22797919","id":"PMC_22797919","title":"PKD2 and PKD3 promote prostate cancer cell invasion by modulating NF-κB- and HDAC1-mediated expression and activation of uPA.","date":"2012","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/22797919","citation_count":85,"is_preprint":false},{"pmid":"34433666","id":"PMC_34433666","title":"TRIM47 activates NF-κB signaling via PKC-ε/PKD3 stabilization and contributes to endocrine therapy resistance in breast cancer.","date":"2021","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/34433666","citation_count":60,"is_preprint":false},{"pmid":"24337579","id":"PMC_24337579","title":"Elevated protein kinase D3 (PKD3) expression supports proliferation of triple-negative breast cancer cells and contributes to mTORC1-S6K1 pathway activation.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24337579","citation_count":48,"is_preprint":false},{"pmid":"27743381","id":"PMC_27743381","title":"Snail-activated long non-coding RNA PCA3 up-regulates PRKD3 expression by miR-1261 sponging, thereby promotes invasion and migration of prostate cancer cells.","date":"2016","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/27743381","citation_count":48,"is_preprint":false},{"pmid":"31387939","id":"PMC_31387939","title":"The kinase PKD3 provides negative feedback on cholesterol and triglyceride synthesis by suppressing insulin signaling.","date":"2019","source":"Science signaling","url":"https://pubmed.ncbi.nlm.nih.gov/31387939","citation_count":30,"is_preprint":false},{"pmid":"31772672","id":"PMC_31772672","title":"Interplay of PKD3 with SREBP1 Promotes Cell Growth via Upregulating Lipogenesis in Prostate Cancer Cells.","date":"2019","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/31772672","citation_count":30,"is_preprint":false},{"pmid":"23760289","id":"PMC_23760289","title":"Evidence of a third ADPKD locus is not supported by re-analysis of designated PKD3 families.","date":"2013","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/23760289","citation_count":29,"is_preprint":false},{"pmid":"19028687","id":"PMC_19028687","title":"PKD3 is the predominant protein kinase D isoform in mouse exocrine pancreas and promotes hormone-induced amylase secretion.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19028687","citation_count":28,"is_preprint":false},{"pmid":"33692335","id":"PMC_33692335","title":"PKD3 promotes metastasis and growth of oral squamous cell carcinoma through positive feedback regulation with PD-L1 and activation of ERK-STAT1/3-EMT signalling.","date":"2021","source":"International journal of oral science","url":"https://pubmed.ncbi.nlm.nih.gov/33692335","citation_count":26,"is_preprint":false},{"pmid":"22893698","id":"PMC_22893698","title":"GIT1 phosphorylation on serine 46 by PKD3 regulates paxillin trafficking and cellular protrusive activity.","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22893698","citation_count":23,"is_preprint":false},{"pmid":"26426580","id":"PMC_26426580","title":"Lack of PRKD2 and PRKD3 kinase domain somatic mutations in PRKD1 wild-type classic polymorphous low-grade adenocarcinomas of the salivary gland.","date":"2016","source":"Histopathology","url":"https://pubmed.ncbi.nlm.nih.gov/26426580","citation_count":21,"is_preprint":false},{"pmid":"31745977","id":"PMC_31745977","title":"The GEF-H1/PKD3 signaling pathway promotes the maintenance of triple-negative breast cancer stem cells.","date":"2019","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/31745977","citation_count":19,"is_preprint":false},{"pmid":"27515283","id":"PMC_27515283","title":"Phos-tag SDS-PAGE resolves agonist- and isoform-specific activation patterns for PKD2 and PKD3 in cardiomyocytes and cardiac fibroblasts.","date":"2016","source":"Journal of molecular and cellular cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/27515283","citation_count":18,"is_preprint":false},{"pmid":"27245420","id":"PMC_27245420","title":"PKD3 deficiency causes alterations in microtubule dynamics during the cell cycle.","date":"2016","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/27245420","citation_count":14,"is_preprint":false},{"pmid":"34145024","id":"PMC_34145024","title":"A phosphoproteomic approach reveals that PKD3 controls PKA-mediated glucose and tyrosine metabolism.","date":"2021","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/34145024","citation_count":13,"is_preprint":false},{"pmid":"33378018","id":"PMC_33378018","title":"PRKD3 promotes malignant progression of OSCC by downregulating KLF16 expression.","date":"2020","source":"European review for medical and pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33378018","citation_count":11,"is_preprint":false},{"pmid":"15927450","id":"PMC_15927450","title":"Individual C1 domains of PKD3 in phorbol ester-induced plasma membrane translocation of PKD3 in intact cells.","date":"2005","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/15927450","citation_count":11,"is_preprint":false},{"pmid":"20621130","id":"PMC_20621130","title":"A role for PKD1 and PKD3 activation in modulation of calcium oscillations induced by orexin receptor 1 stimulation.","date":"2010","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/20621130","citation_count":9,"is_preprint":false},{"pmid":"36672148","id":"PMC_36672148","title":"Protein Kinase D3 (PKD3) Requires Hsp90 for Stability and Promotion of Prostate Cancer Cell Migration.","date":"2023","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/36672148","citation_count":6,"is_preprint":false},{"pmid":"35440091","id":"PMC_35440091","title":"Addressing the role of PKD3 in the T cell compartment with knockout mice.","date":"2022","source":"Cell communication and signaling : 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sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39859313","citation_count":1,"is_preprint":false},{"pmid":"41225782","id":"PMC_41225782","title":"Primary Sweat Gland Adenocarcinoma of the Skin With ATL2::PRKD3 Fusion: A Potential Cutaneous Analog of Cribriform Adenocarcinoma of the Salivary Glands?","date":"2025","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/41225782","citation_count":1,"is_preprint":false},{"pmid":"38798068","id":"PMC_38798068","title":"T cell-intrinsic PKD3 fine-tunes differentiation into CD8+ central memory T cells and CD8 single positive thymocyte development.","date":"2024","source":"Immunology","url":"https://pubmed.ncbi.nlm.nih.gov/38798068","citation_count":0,"is_preprint":false},{"pmid":"40970203","id":"PMC_40970203","title":"PKD3 localizes to late endosomes to maintain Rab7-dependent endolysosomal homeostasis.","date":"2025","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/40970203","citation_count":0,"is_preprint":false},{"pmid":"41980898","id":"PMC_41980898","title":"PRKD3 Overexpression May Improve Survival and Suppresses Proliferation in Colorectal Cancer.","date":"2026","source":"Cancer reports (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/41980898","citation_count":0,"is_preprint":false},{"pmid":"20813663","id":"PMC_20813663","title":"[PKD3 contributes to up-regulation of prostate-specific antigen in prostate cancer cells].","date":"2010","source":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/20813663","citation_count":0,"is_preprint":false},{"pmid":"41928531","id":"PMC_41928531","title":"[Effect of Trifolium repens extract on OSC-4 cell proliferation, apoptosis and NLRP3/PRKD3 protein level].","date":"2026","source":"Shanghai kou qiang yi xue = Shanghai journal of stomatology","url":"https://pubmed.ncbi.nlm.nih.gov/41928531","citation_count":0,"is_preprint":false},{"pmid":"41655233","id":"PMC_41655233","title":"Targeting PRKCN, an Essential Driver Orchestrating mTOR-IRF4 Axis Independently of Kinase Activity, in Multiple Myeloma.","date":"2026","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/41655233","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.05.09.653063","title":"Phosphorylation of the α subunit inhibits proteasome assembly and regulates cell division in an archaeon","date":"2025-05-12","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.09.653063","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.29.610294","title":"Adipose tissue protein kinase D (PKD): regulation of signalling networks and its sex-dependent effects on metabolism","date":"2024-08-30","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.29.610294","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19058,"output_tokens":4843,"usd":0.064909,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13092,"output_tokens":3574,"usd":0.077405,"stage2_stop_reason":"end_turn"},"total_usd":0.142314,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"PKD3 promotes prostate cancer cell growth and survival through a PKCε/PKD3 pathway downstream of Akt and ERK1/2. PKCε regulates PKD3 kinase activity and nuclear localization in PC3 and DU145 cells. Overexpression of PKD3 blocks PMA-induced apoptosis, prolonged ERK1/2 activation, and promotes S phase entry; depletion causes G0-G1 arrest. PKD3-mediated Akt upregulation requires PI3K and p38.\",\n      \"method\": \"Overexpression and siRNA knockdown of PKD3, cell cycle analysis, kinase activity assays, Western blotting for Akt and ERK1/2, immunohistochemistry for subcellular localization\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (KD/OE, cell cycle, kinase activity), single lab\",\n      \"pmids\": [\"18483269\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PKD3 promotes prostate cancer cell invasion by phosphorylating Ser536 on p65 NF-κB, thereby activating uPA transcription. PKD3 also interacts with and suppresses HDAC1, reducing HDAC1 binding to the uPA promoter and thus de-repressing uPA expression. PKD3 interacts physically with IKKβ.\",\n      \"method\": \"siRNA knockdown of PKD2/PKD3, Co-IP (PKD3–IKKβ and PKD3–HDAC1 interactions), ChIP for p65 binding to uPA promoter, rescue experiments with constitutive Ser536 p65 and p65 overexpression, invasion/migration assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, ChIP, epistatic rescue experiments, multiple orthogonal methods in single lab\",\n      \"pmids\": [\"22797919\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM47 forms a ternary complex with PKCε and PKD3, stabilizing both kinases. TRIM47 promotes lysine-27-linked polyubiquitination of PKCε, and this complex activates NF-κB signaling to drive breast cancer proliferation and endocrine therapy resistance.\",\n      \"method\": \"Co-immunoprecipitation (TRIM47–PKCε–PKD3 complex), ubiquitination assays, overexpression and siRNA knockdown in MCF-7 and OHTR cells, proliferation assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ubiquitination assays, single lab, two orthogonal methods\",\n      \"pmids\": [\"34433666\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"PKD3 activates S6K1 (a downstream target of mTORC1) in triple-negative breast cancer cells. PKD3 knockdown reduces S6K1 phosphorylation, impairs mTORC1 activation at endolysosomal membranes, causes accumulation of mannose-6-phosphate receptor, and recruits the autophagy marker LC3 to enlarged acidic vesicles.\",\n      \"method\": \"Antibody array, siRNA knockdown, Western blotting for S6K1 phosphorylation, immunofluorescence for endolysosomal markers and LC3\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — antibody array plus mechanistic follow-up with KD and imaging, single lab\",\n      \"pmids\": [\"24337579\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PKD3 directly phosphorylates GIT1 on serine 46. This phosphorylation acts as a molecular switch that shifts GIT1 localization from focal adhesions to motile, paxillin-positive cytoplasmic complexes, thereby regulating paxillin trafficking and cellular protrusive activity.\",\n      \"method\": \"Mass spectrometry-based phosphoproteomics to identify GIT1 S46 as PKD3 substrate, siRNA knockdown of PKD3, phosphomimetic (S46D) and phospho-deficient (S46A) GIT1 mutants, immunofluorescence imaging of GIT1 localization and paxillin\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct substrate identification by MS, mutagenesis-based functional validation, mechanistic imaging readout\",\n      \"pmids\": [\"22893698\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PKD3 is the predominant PKD isoform in hepatocytes and provides negative feedback on insulin signaling by suppressing AKT, mTORC1, and mTORC2 activity. Hepatic deletion of PKD3 in mice improves insulin-induced glucose tolerance but increases SREBP-mediated lipogenesis and hepatic triglyceride/cholesterol content on a high-fat diet. Constitutively active PKD3 overexpression causes insulin resistance.\",\n      \"method\": \"Hepatic-specific PKD3 knockout mouse, constitutively active PKD3 overexpression mouse model, glucose tolerance tests, Western blotting for AKT/mTORC1/mTORC2, SREBP pathway analysis, lipid measurements\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo genetic loss-of-function and gain-of-function mouse models, multiple orthogonal metabolic readouts, replicated across conditions\",\n      \"pmids\": [\"31387939\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PKD3 interacts with SREBP1 in prostate cancer cells, promotes maturation of SREBP1 (68 kDa form), and enhances SREBP1 binding to the FASN promoter to upregulate de novo lipogenesis. PKD3 silencing reduces lipid content and expression of FASN and ACLY; overexpression of SREBP1 rescues the growth suppression caused by PKD3 depletion.\",\n      \"method\": \"Co-immunoprecipitation (PKD3–SREBP1), ChIP (SREBP1 at FASN promoter), siRNA knockdown, SREBP1 overexpression rescue, lipid content assays, Western blotting\",\n      \"journal\": \"Journal of Cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ChIP, epistatic rescue, single lab\",\n      \"pmids\": [\"31772672\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PKD3 is the predominant PKD isoform in mouse exocrine pancreatic acinar cells. It undergoes rapid membrane translocation, trans-activating phosphorylation, and kinase activation after gastrointestinal hormone or cholinergic stimulation via a Ca2+-independent, diacylglycerol- and PKC-dependent mechanism. PKD3 activation potentiates MEK/ERK/RSK signaling and enhances cholecystokinin-mediated amylase secretion.\",\n      \"method\": \"Differential PKD isoform expression analysis, membrane fractionation/translocation assays, pharmacological PKC inhibition, ERK/RSK Western blotting, amylase secretion assay in isolated acinar cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods in isolated primary acinar cells, single lab\",\n      \"pmids\": [\"19028687\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"The C1a domain of PKD3 is responsible for high-affinity phorbol ester ([3H]PDBu) binding, while C1b has no detectable binding activity. Both C1a and PKD3 kinase activity are required for phorbol ester (PMA)-induced plasma membrane translocation of PKD3. PKC, by directly activating PKD3, regulates its plasma membrane localization.\",\n      \"method\": \"Radioligand binding assay ([3H]PDBu), C1a/C1b point mutations, GFP-tagged PKD3 live-cell imaging, constitutively active and kinase-dead PKD3 constructs, PKC inhibitor RO 31-8220\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro binding assay with mutagenesis, live-cell translocation imaging, pharmacological validation, multiple orthogonal approaches\",\n      \"pmids\": [\"15927450\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PKD3 co-localizes with the androgen receptor (AR) in the nucleus of LNCaP cells after DHT stimulation. Wild-type PKD3 significantly increases AR transcriptional activity and PSA expression in response to DHT; kinase-dead PKD3 partially reduces AR transcriptional activity, indicating kinase activity is required.\",\n      \"method\": \"Dual-luciferase AR reporter assay, RT-QPCR for PSA mRNA, confocal microscopy for PKD3/AR co-localization, overexpression of wild-type vs. kinase-dead PKD3\",\n      \"journal\": \"Nan fang yi ke da xue xue bao (Journal of Southern Medical University)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reporter assay, co-localization imaging, kinase-dead mutant, single lab\",\n      \"pmids\": [\"20813663\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PKD3 deficiency in mouse embryonic fibroblasts impairs microtubule nucleation and dynamics during the cell cycle. PKD1 can partially compensate for PKD3 function in this process.\",\n      \"method\": \"Genetic PKD3 knockout MEFs, microtubule nucleation and dynamics assays, cell cycle analysis\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO model with specific cellular phenotype, single lab\",\n      \"pmids\": [\"27245420\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PKD2 and PKD3 are activated in cardiomyocytes and cardiac fibroblasts by sphingosine-1-phosphate, thrombin, PDGF, and H2O2 via PKC-dependent pathways. A novel role for Rho was identified in sphingosine-1-phosphate and thrombin receptor-dependent activation of PKD2/3 and downstream CREB phosphorylation in cardiomyocytes.\",\n      \"method\": \"Phos-tag SDS-PAGE, PKC inhibitor GF109203X, Rho inhibitor C3 toxin, CREB phosphorylation assays, in isolated cardiac fibroblasts and cardiomyocytes\",\n      \"journal\": \"Journal of molecular and cellular cardiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Phos-tag SDS-PAGE with pharmacological epistasis, single lab, two cell types\",\n      \"pmids\": [\"27515283\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PKD1 and PKD3 are both activated by orexin-A (via orexin receptor 1) and translocate to the plasma membrane. Overexpression of kinase-dead PKD1 or kinase-dead PKD3 disrupts orexin-A-induced calcium oscillations, demonstrating a functional role for PKD3 kinase activity in modulating Ca2+ responses.\",\n      \"method\": \"Phosphospecific antibody detection of PKD1/PKD3 activation, dominant-negative (kinase-dead) PKD1 and PKD3 overexpression, intracellular calcium imaging in HEKOx1R cells\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — kinase-dead dominant negative approach with calcium imaging readout, single lab\",\n      \"pmids\": [\"20621130\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The RhoGEF GEF-H1 acts upstream of PKD3 activation in triple-negative breast cancer stem cells. PKD3 is required for maintenance of the TNBC stem cell population, as its depletion reduces cancer stem cell frequency in vitro and tumor initiation potential in vivo.\",\n      \"method\": \"PKD3 siRNA knockdown, in vitro oncosphere and colony formation assays, in vivo tumor initiation assay, pharmacological PKD inhibition combined with paclitaxel\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KD with in vitro and in vivo functional readouts plus pharmacological validation, single lab\",\n      \"pmids\": [\"31745977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PKD3 activates PKA and regulates PKA-mediated glucose and tyrosine metabolism in hepatocytes. PKD3 is activated by glucagon and promotes glucose and tyrosine levels in hepatocytes. Identified >300 putative PKD3 substrates by phosphoproteomics, including phenylalanine hydroxylase (PAH) as a downstream PKA target.\",\n      \"method\": \"Phosphoproteomics on PKD3-deficient hepatocytes, biochemical PKA activity assays, glucagon stimulation, glucose and tyrosine metabolite measurements\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phosphoproteomics plus biochemical validation, single lab\",\n      \"pmids\": [\"34145024\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Hsp90 physically interacts with PKD3 to ensure its conformational stability. Pharmacological Hsp90 inhibition causes proteasomal degradation of PKD3 and abrogates PKD3-dependent prostate cancer cell migration. PKD3 is thus an Hsp90 client protein.\",\n      \"method\": \"Proximity ligation assay, co-immunoprecipitation (Hsp90–PKD3), Hsp90 inhibitor (ganetespib) treatment, proteasome inhibition rescue, PKD3 siRNA combined with ganetespib, ectopic PKD3 overexpression in LNCaP cells\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus PLA plus functional rescue, single lab\",\n      \"pmids\": [\"36672148\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PRKCN (PKD3) physically interacts with mTOR and activates mTORC1/C2 signaling to sustain IRF4 expression in multiple myeloma. PRKCN and IRF4 form a feed-forward transcriptional circuit: IRF4 directly induces PRKCN transcription, and PRKCN fosters IRF4 expression via mTOR. This function is independent of PKD3 kinase activity but requires activation-loop phosphorylation.\",\n      \"method\": \"Co-immunoprecipitation (PRKCN–mTOR), constitutive/inducible knockdown, kinase-dead mutant analysis, ChIP-seq/luciferase for IRF4-PRKCN circuit, in vivo xenograft models, pharmacological PRKCN inhibitor\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, kinase-dead mutant, in vivo xenograft validation, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"41655233\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Endogenous PKD3 localizes to Rab7-positive late endosomes in MDA-MB-231 TNBC cells cultured on stiff matrices. PKD3 depletion results in smaller Rab7-positive vesicles, reduced retromer complex recruitment, enhanced cathepsin D secretion, impaired endosomal acidification, dysregulated Wnt signaling, and a decline in cancer stemness.\",\n      \"method\": \"Endogenous PKD3 localization by immunofluorescence, siRNA PKD3 knockdown, Rab7 vesicle size quantification, retromer recruitment assay, cathepsin D secretion assay, endosomal pH measurement, Wnt signaling and stemness assays\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment tied to functional consequence with multiple orthogonal readouts, single lab\",\n      \"pmids\": [\"40970203\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PRKD3 (PKD3) is a DAG/phorbol ester-activated serine-threonine kinase whose C1a domain mediates membrane recruitment; it is activated downstream of PKC (and Rho in some contexts) and operates at multiple subcellular compartments—plasma membrane, Golgi, nucleus, and Rab7-positive late endosomes—where it phosphorylates substrates including GIT1-S46 (regulating focal adhesion dynamics), p65 NF-κB-S536 (promoting uPA transcription and invasion), and interacts with SREBP1, HDAC1, IKKβ, mTOR, and Hsp90 to coordinate cell proliferation, survival, lipogenesis, insulin feedback, endolysosomal homeostasis, and cancer stem cell maintenance.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PRKD3 (PKD3) is a diacylglycerol/phorbol ester-responsive serine-threonine kinase that acts as a downstream effector of protein kinase C to couple receptor and lipid signaling to proliferation, survival, metabolism, and invasion across multiple tissues [#0, #7, #8]. Its C1a domain mediates high-affinity phorbol ester binding, and both C1a and intrinsic kinase activity are required for PMA-induced plasma-membrane translocation, with PKC directly activating PKD3 to control its localization [#8]; activation downstream of PKC (and, in cardiomyocytes, Rho) is broadly elicited by hormonal, cholinergic, and growth-factor stimuli [#7, #11, #12]. Once activated, PKD3 drives a pro-invasive transcriptional program by phosphorylating p65 NF-\\u03baB on Ser536 and suppressing HDAC1 to de-repress uPA, and it directly phosphorylates GIT1 on Ser46 to shift GIT1 between focal adhesions and motile paxillin-positive complexes, linking the kinase to focal-adhesion dynamics and cell motility [#1, #4]. PKD3 also governs lipid and glucose metabolism: it interacts with SREBP1 to promote its maturation and FASN-driven lipogenesis in prostate cancer, and in hepatocytes it is the predominant isoform, exerting negative feedback on AKT/mTORC1/mTORC2 insulin signaling while activating PKA-mediated glucose and tyrosine metabolism [#5, #6, #14]. In cancer, PKD3 supports mTORC1/mTORC2 signaling at endolysosomal membranes, localizes to Rab7-positive late endosomes to sustain retromer recruitment and endosomal acidification, and maintains triple-negative breast cancer and multiple myeloma stem/tumor-initiating populations, in part through an IRF4 feed-forward circuit and Hsp90-dependent stabilization [#3, #13, #15, #16, #17].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established the structural basis for PKD3 membrane recruitment, answering how the kinase senses lipid second messengers and is positioned at the plasma membrane.\",\n      \"evidence\": \"Radioligand binding with C1a/C1b mutants and live-cell imaging of GFP-PKD3 with PKC inhibition\",\n      \"pmids\": [\"15927450\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define which substrates are phosphorylated at the membrane\", \"Structural model of the activated kinase not resolved\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defined PKD3 as a pro-growth, pro-survival effector in a PKC\\u03b5/PKD3 axis, framing its role in cell-cycle progression and apoptosis resistance.\",\n      \"evidence\": \"Overexpression/siRNA in prostate cancer cells with cell-cycle, kinase-activity, and ERK/Akt readouts\",\n      \"pmids\": [\"18483269\", \"19028687\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct nuclear substrates not identified\", \"Mechanism of nuclear localization control unresolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified two direct mechanistic outputs of PKD3 — transcriptional de-repression of uPA via p65/HDAC1 and a direct GIT1-S46 phosphorylation switch — connecting the kinase to invasion and focal-adhesion dynamics.\",\n      \"evidence\": \"Reciprocal Co-IP, ChIP, epistatic rescue, and MS-based substrate identification with phosphomimetic mutants\",\n      \"pmids\": [\"22797919\", \"22893698\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether p65-S536 is a direct PKD3 substrate vs. indirect not fully separated\", \"GIT1-S46 switch not validated in vivo\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Placed PKD3 upstream of mTORC1 at endolysosomal membranes, linking it to autophagy and lysosomal homeostasis in TNBC.\",\n      \"evidence\": \"Antibody array, siRNA knockdown, and immunofluorescence for endolysosomal/LC3 markers\",\n      \"pmids\": [\"24337579\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mTORC1-pathway substrate of PKD3 not identified\", \"Mechanism of endolysosomal recruitment unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed PKD3 as a tissue-specific metabolic regulator and a lipogenesis driver, showing context-dependent suppression of insulin signaling in liver versus SREBP1-driven lipogenesis in cancer.\",\n      \"evidence\": \"Hepatic knockout/constitutively-active mouse models with metabolic readouts, and Co-IP/ChIP/rescue for SREBP1-FASN in prostate cancer\",\n      \"pmids\": [\"31387939\", \"31772672\", \"31745977\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct PKD3 phosphorylation sites on insulin-pathway components not mapped\", \"Reconciliation of pro- vs anti-mTOR roles across tissues incomplete\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Expanded PKD3 regulatory inputs and outputs, identifying TRIM47-mediated kinase stabilization and a glucagon/PKA metabolic branch with a large putative substrate set.\",\n      \"evidence\": \"Co-IP, ubiquitination assays in breast cancer cells, and phosphoproteomics with PKA biochemical validation in hepatocytes\",\n      \"pmids\": [\"34433666\", \"34145024\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Most of the >300 putative substrates not individually validated\", \"Direct vs PKA-mediated phosphorylation events not distinguished\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established PKD3 as an Hsp90 client whose stability is chaperone-dependent, identifying a druggable vulnerability for PKD3-driven migration.\",\n      \"evidence\": \"PLA, reciprocal Co-IP, Hsp90 inhibition with proteasome-rescue in prostate cancer cells\",\n      \"pmids\": [\"36672148\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Hsp90 co-chaperone requirements not defined\", \"Effect on other PKD3 functions beyond migration untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolved an endosomal function for endogenous PKD3 at Rab7-positive late endosomes governing retromer recruitment, acidification, and stemness, anchoring earlier endolysosomal phenotypes to a defined compartment.\",\n      \"evidence\": \"Endogenous immunofluorescence localization plus retromer, cathepsin D secretion, endosomal pH, and Wnt/stemness assays in TNBC\",\n      \"pmids\": [\"40970203\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Endosomal PKD3 substrates not identified\", \"Mechanism coupling PKD3 to retromer recruitment unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined a kinase-activity-independent scaffolding role for PKD3 in an mTOR/IRF4 feed-forward circuit sustaining multiple myeloma, showing PKD3 functions extend beyond catalysis.\",\n      \"evidence\": \"Co-IP with mTOR, kinase-dead mutant analysis, ChIP-seq/luciferase, and xenograft models\",\n      \"pmids\": [\"41655233\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How activation-loop phosphorylation enables kinase-independent function unclear\", \"Direct PKD3-mTOR binding interface not mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The unifying logic that determines which PKD3 outputs (transcriptional, metabolic, endosomal, scaffolding) dominate in a given cell type, and the full direct substrate repertoire, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No comprehensive validated direct substrate map\", \"Context-dependent compartment selection mechanism unknown\", \"No structural model of activated full-length PKD3\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [4, 8]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 9, 16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [8, 12]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [3, 17]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 7, 11]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [5, 6, 14]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 9, 16]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [13, 16, 17]}\n    ],\n    \"complexes\": [\"TRIM47-PKCε-PKD3 complex\"],\n    \"partners\": [\"IKKβ\", \"HDAC1\", \"SREBP1\", \"TRIM47\", \"PKCε\", \"HSP90\", \"MTOR\", \"GIT1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}