{"gene":"STK38L","run_date":"2026-04-28T21:42:57","timeline":{"discoveries":[{"year":2004,"finding":"Human NDR2 (STK38L) forms stable complexes with human Mob2 protein, and this association dramatically stimulates NDR2 catalytic activity, identifying Mob proteins as kinase-activating subunits for NDR1 and NDR2.","method":"Co-immunoprecipitation from Jurkat T-cells, colocalization in HeLa cells, in vitro kinase activity assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP plus functional kinase activity assay, replicated across cell types","pmids":["15067004"],"is_preprint":false},{"year":2004,"finding":"NDR2 is activated by multi-site phosphorylation: Ser-282 undergoes autophosphorylation in vivo (activation segment), while Thr-442 (hydrophobic motif) is targeted by an upstream kinase; S100B calcium-binding protein stimulates NDR2 autophosphorylation in vitro.","method":"In vitro kinase assay, phospho-site mutagenesis, okadaic acid treatment, constitutively active chimeric kinase construction","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro kinase assay with mutagenesis and multiple orthogonal methods","pmids":["15037617"],"is_preprint":false},{"year":2004,"finding":"NDR2 exhibits a predominant cytoplasmic (non-nuclear) localization, in contrast to NDR1 which localizes to the nucleus, indicating distinct subcellular distributions for the two isoforms.","method":"Fluorescence microscopy of ectopically expressed tagged proteins in HeLa/COS cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — direct localization by imaging, replicated in multiple studies","pmids":["15037617","15067004"],"is_preprint":false},{"year":2004,"finding":"Ndr2 associates with the actin cytoskeleton in somata, neurites, filopodia, spines, and sites of cell contact in PC12 cells and cortical neurons; kinase expression causes decreased cell spreading, changes in neurite outgrowth, and protein serine phosphorylation.","method":"EGFP fusion protein expression, co-precipitation and pull-down with actin, fluorescence microscopy","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 — single lab pulldown plus functional morphological readout","pmids":["15308672"],"is_preprint":false},{"year":2005,"finding":"NDR2 is incorporated into HIV-1 virions and cleaved by the HIV-1 protease; truncation at the protease cleavage site alters NDR2 subcellular localization and inhibits NDR2 enzymatic activity.","method":"Virion fractionation, in vitro HIV-1 protease cleavage assay, subcellular localization microscopy, kinase activity assay","journal":"Virology","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro protease assay with functional kinase readout and localization data","pmids":["15582665"],"is_preprint":false},{"year":2006,"finding":"NDR2 acts as an upstream kinase for ARK5 during IGF-1 signaling: upon IGF-1 stimulation, NDR2 directly phosphorylates Thr-211 on the ARK5 activation T-loop, promoting ARK5-mediated cell survival and invasion; NDR2 activation requires phosphorylation at Thr-75, Ser-282, and Thr-442, with PDK-1 playing a role in Thr-442 phosphorylation.","method":"In vitro kinase assay, phospho-site mutagenesis, IGF-1 stimulation, cell survival and invasion assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — direct in vitro phosphorylation assay with mutagenesis and functional cellular readout","pmids":["16488889"],"is_preprint":false},{"year":2013,"finding":"NDR2 phosphorylates Rabin8 at Ser-272, which switches Rabin8 binding specificity from phosphatidylserine to Sec15 (exocyst component), thereby promoting Rab8 activation and ciliary membrane formation; loss of this phosphorylation impairs preciliary membrane assembly and ciliogenesis.","method":"In vitro kinase assay, phospho-mimetic and non-phosphorylatable Rabin8 mutants, ciliogenesis assay, lipid binding assay, Co-IP","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 — in vitro phosphorylation plus mutagenesis plus functional ciliogenesis readout, multiple orthogonal methods","pmids":["23435566"],"is_preprint":false},{"year":2014,"finding":"Ndr2 phosphorylates β1-integrin at Thr-788/789 to stimulate PKC- and CaMKII-dependent β1-integrin activation and exocytosis; Ndr2 associates with integrin-positive early and recycling endosomes in hippocampal neurons; Ndr2 knockout mice show reduced surface expression of activated β1-integrins on dendrites and altered dendritic complexity in the hippocampus.","method":"In vitro phosphorylation assay, endosome fractionation, surface biotinylation, constitutive knockout mouse, immunofluorescence","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro kinase assay, subcellular fractionation, KO mouse with defined cellular phenotype","pmids":["24719112"],"is_preprint":false},{"year":2017,"finding":"NDR2 localizes to peroxisomes via a C-terminal GKL sequence (PTS1-like motif) recognized by the PTS1 receptor Pex5p; this peroxisomal localization (absent in the NDR2-ΔL mutant lacking the C-terminal Leu) is required for NDR2's function in promoting primary ciliogenesis.","method":"Fluorescence microscopy colocalization with peroxisome markers, Pex5p binding assay, ciliogenesis rescue experiment with NDR2-ΔL mutant, PEX gene knockdown","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — receptor binding assay plus mutagenesis plus functional rescue experiment","pmids":["28122914"],"is_preprint":false},{"year":2018,"finding":"Ndr2 becomes activated upon TCR stimulation and phosphorylates Filamin A (FLNa) at Ser-2152, promoting FLNa dissociation from LFA-1 and subsequent Talin/Kindlin-3 association that stabilizes the open (active) LFA-1 conformation in T cells.","method":"In vitro kinase assay, phospho-mimetic mutants, Co-IP, T-cell activation assays, LFA-1 conformation assay","journal":"Frontiers in immunology","confidence":"High","confidence_rationale":"Tier 1–2 — direct in vitro phosphorylation with functional LFA-1 activation readout and Co-IP","pmids":["30568657"],"is_preprint":false},{"year":2019,"finding":"NDR2 directly associates with both RIG-I and TRIM25, facilitating formation of the RIG-I/TRIM25 complex and enhancing TRIM25-mediated K63-linked polyubiquitination of RIG-I, which is required for RIG-I-mediated antiviral immune signaling; NDR2 conditional knockout mice show impaired antiviral responses.","method":"Co-IP, overexpression of kinase-inactive mutants, conditional knockout mice (Lysm+NDR2f/f), ubiquitination assay","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, ubiquitination assay, and conditional KO mouse with defined phenotype","pmids":["30775439"],"is_preprint":false},{"year":2019,"finding":"NDR2 directly interacts with GEF-H1 and phosphorylates it (at an NDR consensus motif HXRXXS/T), leading to RhoB GTPase inactivation; upon RASSF1A loss, this NDR2/GEF-H1/RhoB/YAP axis drives migration, metastasis, and cytokinesis defects in bronchial cells.","method":"Co-IP, siRNA/shRNA knockdown, phosphorylation assay, xenograft assay, genetic epistasis by sequential knockdown","journal":"Journal of experimental & clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — direct Co-IP plus functional epistasis, single lab","pmids":["30979377"],"is_preprint":false},{"year":2018,"finding":"NDR2 interacts with E3 ubiquitin ligase Smurf1 and promotes Smurf1-mediated K48-linked ubiquitination of MEKK2, leading to MEKK2 degradation and inhibition of IL-17-induced inflammatory signaling.","method":"Co-IP, ubiquitination assay, siRNA knockdown, cytokine expression assays","journal":"Molecular immunology","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus ubiquitination assay, single lab","pmids":["30504095"],"is_preprint":false},{"year":2019,"finding":"NDR2 can be acetylated at K463; SIRT1 acts as the major deacetylase for NDR2, while p300 and CBP function as acetyltransferases; in SIRT1-deficient cells, HDAC6 and HDAC1/2 can deacetylate NDR2.","method":"Mass spectrometry identification of acetylation site, co-immunoprecipitation with acetyltransferases/deacetylases, SIRT1 knockout cell experiments","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP with functional deacetylase identification plus site-specific modification mapping","pmids":["31427083"],"is_preprint":false},{"year":2022,"finding":"TRIM27 catalyzes K6- and K11-linked (non-degradative) ubiquitination of STK38L during starvation-induced autophagy, which promotes STK38L activation; activated STK38L then phosphorylates ULK1 at Ser-495, rendering ULK1 permissive for TRIM27-mediated K48-linked hyper-ubiquitination and proteasomal degradation, thereby restraining autophagy amplitude and duration.","method":"In vitro ubiquitination assay, in vitro kinase assay, Co-IP, site-directed mutagenesis, Trim27 knockout mice","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro ubiquitination and kinase assays, mutagenesis, KO mouse model, multiple orthogonal methods","pmids":["35670107"],"is_preprint":false},{"year":2022,"finding":"STK38L (NDR2), induced by serum response factor (SRF) in response to lysophosphatidic acid (LPA), phosphorylates IRF3 at Ser-303, preventing IRF3 from proteasome-mediated degradation in the resting state, thereby maintaining sufficient IRF3 levels for rapid antiviral responses; STK38L-deficient mice show compromised innate antiviral responses.","method":"In vitro kinase assay, phospho-site mutagenesis, STK38L-knockout mice, IRF3 stability assay, viral challenge experiments","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1–2 — direct phosphorylation assay with mutagenesis, KO mouse with defined antiviral phenotype","pmids":["36417850"],"is_preprint":false},{"year":2017,"finding":"STK38L depletion in KRAS-dependent PDAC cells (ADEX subtype) inhibits proliferation, induces apoptosis, and increases LATS2 kinase and p21 expression; LATS2 depletion partially rescues these effects, placing STK38L upstream of LATS2 in a pathway controlling PDAC cell viability.","method":"RNAi knockdown, genetic epistasis by double knockdown, apoptosis assay, cell proliferation assay","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis by double knockdown with defined cellular phenotype","pmids":["29108249"],"is_preprint":false},{"year":2024,"finding":"NDR2 (STK38L) promotes autophagy and mitophagy by mediating ULK1 instability, thereby acting as a negative regulator of osteoclastogenesis; myeloid-specific NDR2 knockout mice show lower bone mass and exacerbated bone loss, and ULK1 inhibition ameliorates the bone loss caused by NDR2 conditional knockout.","method":"Conditional knockout mice (Lysm+NDR2fl/fl), ULK1 stability assay, autophagy/mitophagy assays, ULK1 inhibitor rescue experiment","journal":"JCI insight","confidence":"Medium","confidence_rationale":"Tier 2 — conditional KO mouse with defined phenotype plus pharmacological rescue, single lab","pmids":["39561008"],"is_preprint":false},{"year":2024,"finding":"SENP2 de-SUMOylates NDR2 at K463 (or nearby site), which improves NDR2 kinase activity; activated NDR2 then destabilizes p21, accelerating the G1/S cell cycle transition in lung cancer cells.","method":"Co-IP, SUMO deconjugation assay, kinase activity assay, cell cycle analysis, siRNA knockdown","journal":"European journal of pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical de-SUMOylation assay with functional kinase activity readout, single lab","pmids":["38908669"],"is_preprint":false},{"year":2025,"finding":"NDR2 phosphorylates Rabin8 at S272 at the trans-Golgi/Golgi exit sites (GESs) to regulate Rab11-to-Rab8 succession; NDR2 interacts with VAMP7 at these sites; non-phosphorylatable Rabin8-S272A causes GES enlargement and disrupts rhodopsin Golgi-to-cilia trafficking in Xenopus rod photoreceptors.","method":"Transgenic Xenopus laevis expressing GFP-Rabin8 and phospho-mutants, Co-IP with VAMP7, fluorescence microscopy","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1 — in vivo phospho-mutant analysis in transgenic vertebrate photoreceptors with defined trafficking phenotype","pmids":["39774853"],"is_preprint":false},{"year":2025,"finding":"NDR2 regulates autophagosome formation and distribution in lung cancer cells in an ATG9A-dependent manner, and is required for lysosomal trafficking/fusion with autophagosomes; NDR2 silencing disrupts Golgi repositioning to the leading edge, inhibiting filopodia formation and cell migration under serum deprivation.","method":"siRNA/shRNA knockdown, LC3-II immunoblot, ATG9A functional assay, migration assay, Golgi repositioning microscopy, chloroquine block","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 — multiple functional assays in same cells, single lab","pmids":["41390758"],"is_preprint":false},{"year":2025,"finding":"NDR2 deficiency in hippocampal neurons reduces T788/789-phosphorylated β1-integrin at synaptic sites, decreases synaptic density, and reduces long-term potentiation in CA1 Schaffer collateral synapses; integrin-activating RGD peptide rescues LTP deficits, placing NDR2-mediated integrin phosphorylation upstream of synapse formation and plasticity.","method":"Constitutive NDR2 knockout mice, immunostaining for phospho-β1-integrin, synaptic density quantification, LTP electrophysiology, RGD peptide rescue","journal":"Journal of neurochemistry","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse with electrophysiological and morphological phenotype plus pharmacological rescue, single lab","pmids":["40439020"],"is_preprint":false}],"current_model":"STK38L (NDR2) is a cytoplasmic serine/threonine kinase activated by multi-site phosphorylation (autophosphorylation at Ser-282, upstream kinase input at Thr-442) and by Mob protein binding, that localizes to peroxisomes via a C-terminal PTS1-like GKL motif and phosphorylates multiple substrates—including Rabin8 (Ser-272) to drive ciliogenesis, β1-integrin (Thr-788/789) to promote integrin trafficking and neurite/synapse development, Filamin A (Ser-2152) to initiate LFA-1 activation, ULK1 (Ser-495) to modulate autophagy, IRF3 (Ser-303) to maintain antiviral innate immune readiness, ARK5 (Thr-211) to support tumor cell survival, and GEF-H1 to regulate RhoB and cytokinesis—while its activity is further regulated by TRIM27-mediated ubiquitination, SENP2-mediated de-SUMOylation, and SIRT1/p300-mediated reversible acetylation."},"narrative":{"teleology":[{"year":2004,"claim":"Establishing the activation mechanism of NDR2 resolved how this kinase is switched on: Mob2 binding dramatically stimulates catalytic activity, while Ser-282 autophosphorylation and Thr-442 phosphorylation by an upstream kinase are both required, with S100B additionally stimulating autophosphorylation in vitro.","evidence":"Co-IP from Jurkat T-cells and HeLa cells with in vitro kinase assays, phospho-site mutagenesis, and okadaic acid treatment","pmids":["15067004","15037617"],"confidence":"High","gaps":["The upstream kinase for Thr-442 was not definitively identified in these studies (PDK1 role was implied later)","How Mob2 binding allosterically activates NDR2 structurally is unresolved","Relative contributions of S100B vs. Mob2 in physiological contexts remain unclear"]},{"year":2004,"claim":"Demonstrating that NDR2 is predominantly cytoplasmic and associates with the actin cytoskeleton in neurons established its distinct subcellular context compared to nuclear NDR1 and linked it to neurite morphology.","evidence":"Fluorescence microscopy of tagged proteins in HeLa/COS/PC12 cells and cortical neurons, actin co-precipitation","pmids":["15037617","15067004","15308672"],"confidence":"High","gaps":["Whether actin association is direct or scaffolded was not determined","Specific actin-binding domain not mapped"]},{"year":2006,"claim":"Identifying ARK5 Thr-211 as a direct NDR2 substrate downstream of IGF-1 signaling was the first demonstration of NDR2 phosphorylating a defined substrate in a growth factor pathway relevant to cell survival and invasion.","evidence":"In vitro kinase assay with phospho-site mutagenesis, IGF-1 stimulation, cell survival and invasion assays","pmids":["16488889"],"confidence":"High","gaps":["Whether NDR2–ARK5 axis operates in non-cancer physiological contexts was not tested","PDK1 involvement at Thr-442 was suggested but not directly demonstrated with reconstituted components"]},{"year":2013,"claim":"Showing that NDR2 phosphorylates Rabin8 at Ser-272 to switch its binding from phosphatidylserine to the exocyst subunit Sec15, thereby activating Rab8 and driving ciliary membrane assembly, established NDR2 as a central regulator of ciliogenesis.","evidence":"In vitro kinase assay, phospho-mimetic/non-phosphorylatable Rabin8 mutants, lipid binding assay, ciliogenesis assay, Co-IP","pmids":["23435566"],"confidence":"High","gaps":["The upstream signal triggering NDR2 activation specifically for ciliogenesis was not identified","Whether other NDR family members can compensate was not addressed"]},{"year":2014,"claim":"Demonstrating that Ndr2 phosphorylates β1-integrin at Thr-788/789 on endosomes and that Ndr2 knockout mice have reduced dendritic integrin activation and altered hippocampal morphology revealed a neuronal trafficking function for the kinase.","evidence":"In vitro phosphorylation, endosome fractionation, surface biotinylation, constitutive knockout mouse with hippocampal phenotype","pmids":["24719112"],"confidence":"High","gaps":["Which endosomal sorting machinery cooperates with NDR2-phosphorylated integrins was not defined","Behavioral consequences of altered dendritic complexity were not reported"]},{"year":2017,"claim":"Localizing NDR2 to peroxisomes via its C-terminal PTS1-like GKL motif recognized by Pex5p, and showing this peroxisomal localization is required for ciliogenesis, linked peroxisome biology to ciliary membrane biogenesis through a single kinase.","evidence":"Colocalization with peroxisome markers, Pex5p binding assay, ciliogenesis rescue with NDR2-ΔL mutant, PEX gene knockdown","pmids":["28122914"],"confidence":"High","gaps":["How peroxisomal localization facilitates Rabin8 phosphorylation at ciliary precursor membranes is mechanistically unclear","Whether NDR2 has peroxisome-intrinsic substrates is unknown"]},{"year":2017,"claim":"Placing STK38L upstream of LATS2 in KRAS-dependent pancreatic cancer cells, where its depletion induces apoptosis and p21 upregulation, identified a survival function in PDAC.","evidence":"RNAi epistasis by double knockdown of STK38L and LATS2, apoptosis and proliferation assays","pmids":["29108249"],"confidence":"Medium","gaps":["The direct biochemical mechanism linking STK38L to LATS2 regulation was not established","Generalizability beyond the ADEX PDAC subtype is untested"]},{"year":2018,"claim":"Identifying Filamin A Ser-2152 as a direct NDR2 substrate upon TCR stimulation, with phosphorylation releasing FLNa from LFA-1 to permit talin/kindlin-3 binding, revealed how NDR2 controls integrin inside-out activation in T cells.","evidence":"In vitro kinase assay, phospho-mimetic mutants, Co-IP, LFA-1 conformation assay in T cells","pmids":["30568657"],"confidence":"High","gaps":["How TCR signaling activates NDR2 was not defined","Whether this mechanism operates for integrins beyond LFA-1 is unknown"]},{"year":2018,"claim":"Demonstrating that NDR2 scaffolds Smurf1-mediated K48-ubiquitination and degradation of MEKK2 to suppress IL-17 inflammatory signaling extended NDR2 function to a kinase-independent scaffolding role in innate inflammation.","evidence":"Co-IP, ubiquitination assay, siRNA knockdown, cytokine expression","pmids":["30504095"],"confidence":"Medium","gaps":["Whether NDR2 kinase activity is required for the Smurf1 interaction was not tested","Independent replication needed"]},{"year":2019,"claim":"Showing that NDR2 bridges RIG-I and TRIM25 to enhance K63-polyubiquitination of RIG-I, with conditional knockout mice displaying impaired antiviral responses, established a scaffolding function in innate antiviral immunity.","evidence":"Co-IP, kinase-inactive mutants, ubiquitination assay, Lysm-Cre conditional KO mice with viral challenge","pmids":["30775439"],"confidence":"High","gaps":["Whether kinase activity or only scaffolding is needed for RIG-I activation was not fully resolved","Contribution relative to NDR1 in the same pathway not addressed"]},{"year":2019,"claim":"Identifying GEF-H1 as a direct NDR2 substrate whose phosphorylation inactivates RhoB, driving a RASSF1A-loss-dependent migration and cytokinesis defect axis, connected NDR2 to Rho GTPase regulation in cancer.","evidence":"Co-IP, phosphorylation assay, siRNA epistasis, xenograft assay","pmids":["30979377"],"confidence":"Medium","gaps":["The exact phosphorylation site on GEF-H1 was not fully mapped","Independent validation in non-bronchial cell types is lacking"]},{"year":2019,"claim":"Mapping reversible acetylation of NDR2 at K463 controlled by SIRT1 (deacetylase) and p300/CBP (acetyltransferases) added a post-translational regulatory layer, with HDAC6 and HDAC1/2 serving as backup deacetylases in SIRT1-deficient cells.","evidence":"Mass spectrometry, Co-IP with acetyltransferases/deacetylases, SIRT1 KO cells","pmids":["31427083"],"confidence":"Medium","gaps":["Functional consequence of acetylation on kinase activity or substrate selection was not determined","Whether K463 acetylation and SUMOylation compete at the same residue was not tested"]},{"year":2022,"claim":"Demonstrating that TRIM27 non-degradatively ubiquitinates STK38L (K6/K11 chains) to activate it, after which STK38L phosphorylates ULK1 at Ser-495 to prime ULK1 for TRIM27-mediated K48-ubiquitination and degradation, revealed a feedback circuit that restrains autophagy amplitude.","evidence":"In vitro ubiquitination and kinase assays, mutagenesis, Co-IP, Trim27 KO mice","pmids":["35670107"],"confidence":"High","gaps":["Whether TRIM27-mediated ubiquitination of STK38L is stimulus-specific beyond starvation is unknown","The deubiquitinase counteracting TRIM27 on STK38L was not identified"]},{"year":2022,"claim":"Identifying IRF3 Ser-303 as a direct STK38L substrate that prevents IRF3 proteasomal degradation at steady state, with STK38L-KO mice showing compromised antiviral responses, established STK38L as a constitutive guardian of innate immune readiness.","evidence":"In vitro kinase assay, phospho-site mutagenesis, STK38L-KO mice with viral challenge, IRF3 stability assay","pmids":["36417850"],"confidence":"High","gaps":["The proteasomal pathway that degrades unphosphorylated IRF3 was not identified","Whether NDR1 can partially compensate for IRF3 stabilization is untested"]},{"year":2024,"claim":"Revealing that SENP2-mediated de-SUMOylation at K463 enhances NDR2 kinase activity, which then destabilizes p21 to accelerate G1/S transition, added SUMOylation as a regulatory switch converging on the same residue as acetylation.","evidence":"SUMO deconjugation assay, kinase activity assay, cell cycle analysis, siRNA in lung cancer cells","pmids":["38908669"],"confidence":"Medium","gaps":["The SUMO E3 ligase responsible for NDR2 SUMOylation was not identified","Interplay between SUMOylation, acetylation, and ubiquitination at K463 needs systematic analysis","Independent replication outside lung cancer cells is lacking"]},{"year":2024,"claim":"Conditional myeloid NDR2 knockout mice showing lower bone mass due to enhanced osteoclastogenesis, rescued by ULK1 inhibition, connected the NDR2–ULK1 autophagy axis to bone homeostasis in vivo.","evidence":"Lysm-Cre conditional KO mice, autophagy/mitophagy assays, ULK1 inhibitor rescue","pmids":["39561008"],"confidence":"Medium","gaps":["Whether NDR2 directly phosphorylates ULK1 in osteoclast precursors or acts through TRIM27 was not tested","Single-lab finding awaiting independent replication"]},{"year":2025,"claim":"Showing NDR2 phosphorylates Rabin8 at S272 at trans-Golgi/Golgi exit sites in vertebrate photoreceptors, interacts with VAMP7, and is required for rhodopsin Golgi-to-cilia trafficking extended the Rabin8 phosphorylation mechanism to specialized sensory cilia in vivo.","evidence":"Transgenic Xenopus expressing GFP-Rabin8 phospho-mutants, Co-IP with VAMP7, fluorescence microscopy of rod photoreceptors","pmids":["39774853"],"confidence":"High","gaps":["Whether NDR2 directly binds VAMP7 or is scaffolded remains unclear","Mammalian photoreceptor validation not yet shown"]},{"year":2025,"claim":"Demonstrating that NDR2 deficiency in hippocampal neurons reduces phospho-β1-integrin at synapses, decreases synaptic density, and impairs LTP — rescued by integrin-activating RGD peptide — established NDR2 as essential for synapse formation and plasticity via integrin signaling.","evidence":"Constitutive NDR2 KO mice, phospho-β1-integrin immunostaining, synaptic density quantification, LTP electrophysiology, RGD peptide rescue","pmids":["40439020"],"confidence":"Medium","gaps":["Behavioral consequences (learning/memory) in NDR2 KO mice not reported","Whether NDR2 acts cell-autonomously in postsynaptic neurons vs. presynaptic was not dissected"]},{"year":2025,"claim":"Linking NDR2 to ATG9A-dependent autophagosome formation, lysosomal trafficking, and Golgi repositioning for filopodia-driven migration in lung cancer cells added a migration-autophagy nexus to NDR2 function.","evidence":"siRNA/shRNA knockdown, LC3-II immunoblot, ATG9A functional assay, migration assay, Golgi repositioning microscopy","pmids":["41390758"],"confidence":"Medium","gaps":["Direct substrate linking NDR2 to ATG9A regulation not identified","Relationship to the TRIM27–ULK1 axis not tested","Single-lab finding in cancer cell lines"]},{"year":null,"claim":"How the diverse post-translational modifications of STK38L at K463 (acetylation, SUMOylation) and elsewhere (ubiquitination, phosphorylation) are temporally coordinated to direct substrate selection across its multiple functions — ciliogenesis, autophagy, integrin trafficking, and innate immunity — remains an open question.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of NDR2 with Mob2 or substrates is available","Systematic identification of the full substrate repertoire has not been performed","Relative contributions of NDR1 vs. NDR2 to shared pathways are poorly defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,5,6,7,9,11,14,15,19]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[10,12]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2]},{"term_id":"GO:0005777","term_label":"peroxisome","supporting_discovery_ids":[8]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[3]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[7]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[19]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[5,7,9,11,16]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[10,12,15]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[14,17,20]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[6,8,19]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[18]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[7,21]}],"complexes":[],"partners":["MOB2","TRIM27","RAB3IP","ITGB1","FLNA","IRF3","ULK1","ARHGEF2"],"other_free_text":[]},"mechanistic_narrative":"STK38L (NDR2) is a cytoplasmic serine/threonine kinase of the NDR/LATS family that integrates phosphorylation, ubiquitination, SUMOylation, and acetylation inputs to regulate membrane trafficking, ciliogenesis, autophagy, integrin signaling, and innate immunity. Its catalytic activation requires autophosphorylation at Ser-282, upstream phosphorylation at Thr-442, and binding of Mob2 as an activating subunit, with additional regulation by TRIM27-mediated non-degradative ubiquitination, SENP2-mediated de-SUMOylation, and SIRT1/p300-controlled reversible acetylation at K463 [PMID:15037617, PMID:15067004, PMID:35670107, PMID:38908669, PMID:31427083]. STK38L phosphorylates Rabin8 at Ser-272 to drive Rab8 activation and ciliary membrane assembly from peroxisome-associated and Golgi exit sites, phosphorylates β1-integrin at Thr-788/789 to promote integrin trafficking and synaptic plasticity in hippocampal neurons, phosphorylates Filamin A at Ser-2152 to enable LFA-1 activation in T cells, and phosphorylates IRF3 at Ser-303 to stabilize IRF3 for antiviral innate immune responses [PMID:23435566, PMID:39774853, PMID:24719112, PMID:40439020, PMID:30568657, PMID:36417850]. STK38L also restrains autophagy amplitude by phosphorylating ULK1 at Ser-495, priming it for TRIM27-mediated degradation, scaffolds the RIG-I/TRIM25 complex to potentiate antiviral signaling, and promotes Smurf1-mediated degradation of MEKK2 to dampen IL-17-driven inflammation [PMID:35670107, PMID:39561008, PMID:30775439, PMID:30504095]."},"prefetch_data":{"uniprot":{"accession":"Q9Y2H1","full_name":"Serine/threonine-protein kinase 38-like","aliases":["NDR2 protein kinase","Nuclear Dbf2-related kinase 2"],"length_aa":464,"mass_kda":54.0,"function":"Involved in the regulation of structural processes in differentiating and mature neuronal cells","subcellular_location":"Cytoplasm; Cytoplasm, cytoskeleton; Membrane","url":"https://www.uniprot.org/uniprotkb/Q9Y2H1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/STK38L","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000211455","cell_line_id":"CID001281","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":3},{"compartment":"vesicles","grade":3}],"interactors":[{"gene":"MOB2","stoichiometry":4.0},{"gene":"MOB1A;MOB1B","stoichiometry":0.2},{"gene":"PEX14","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001281","total_profiled":1310},"omim":[{"mim_id":"615836","title":"SERINE/THREONINE PROTEIN KINASE 38-LIKE PROTEIN; STK38L","url":"https://www.omim.org/entry/615836"},{"mim_id":"606964","title":"SERINE/THREONINE PROTEIN KINASE 38; STK38","url":"https://www.omim.org/entry/606964"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"blood vessel","ntpm":80.0}],"url":"https://www.proteinatlas.org/search/STK38L"},"hgnc":{"alias_symbol":["KIAA0965","NDR2"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y2H1","domains":[{"cath_id":"-","chopping":"19-81","consensus_level":"medium","plddt":87.7695,"start":19,"end":81},{"cath_id":"3.30.200.20","chopping":"86-169_405-460","consensus_level":"medium","plddt":79.5954,"start":86,"end":460},{"cath_id":"1.10.510.10","chopping":"174-382","consensus_level":"high","plddt":89.9545,"start":174,"end":382}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2H1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2H1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2H1-F1-predicted_aligned_error_v6.png","plddt_mean":84.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=STK38L","jax_strain_url":"https://www.jax.org/strain/search?query=STK38L"},"sequence":{"accession":"Q9Y2H1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2H1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2H1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2H1"}},"corpus_meta":[{"pmid":"10581191","id":"PMC_10581191","title":"Identification 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chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP plus functional kinase activity assay, replicated across cell types\",\n      \"pmids\": [\"15067004\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"NDR2 is activated by multi-site phosphorylation: Ser-282 undergoes autophosphorylation in vivo (activation segment), while Thr-442 (hydrophobic motif) is targeted by an upstream kinase; S100B calcium-binding protein stimulates NDR2 autophosphorylation in vitro.\",\n      \"method\": \"In vitro kinase assay, phospho-site mutagenesis, okadaic acid treatment, constitutively active chimeric kinase construction\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro kinase assay with mutagenesis and multiple orthogonal methods\",\n      \"pmids\": [\"15037617\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"NDR2 exhibits a predominant cytoplasmic (non-nuclear) localization, in contrast to NDR1 which localizes to the nucleus, indicating distinct subcellular distributions for the two isoforms.\",\n      \"method\": \"Fluorescence microscopy of ectopically expressed tagged proteins in HeLa/COS cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct localization by imaging, replicated in multiple studies\",\n      \"pmids\": [\"15037617\", \"15067004\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Ndr2 associates with the actin cytoskeleton in somata, neurites, filopodia, spines, and sites of cell contact in PC12 cells and cortical neurons; kinase expression causes decreased cell spreading, changes in neurite outgrowth, and protein serine phosphorylation.\",\n      \"method\": \"EGFP fusion protein expression, co-precipitation and pull-down with actin, fluorescence microscopy\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab pulldown plus functional morphological readout\",\n      \"pmids\": [\"15308672\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"NDR2 is incorporated into HIV-1 virions and cleaved by the HIV-1 protease; truncation at the protease cleavage site alters NDR2 subcellular localization and inhibits NDR2 enzymatic activity.\",\n      \"method\": \"Virion fractionation, in vitro HIV-1 protease cleavage assay, subcellular localization microscopy, kinase activity assay\",\n      \"journal\": \"Virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro protease assay with functional kinase readout and localization data\",\n      \"pmids\": [\"15582665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"NDR2 acts as an upstream kinase for ARK5 during IGF-1 signaling: upon IGF-1 stimulation, NDR2 directly phosphorylates Thr-211 on the ARK5 activation T-loop, promoting ARK5-mediated cell survival and invasion; NDR2 activation requires phosphorylation at Thr-75, Ser-282, and Thr-442, with PDK-1 playing a role in Thr-442 phosphorylation.\",\n      \"method\": \"In vitro kinase assay, phospho-site mutagenesis, IGF-1 stimulation, cell survival and invasion assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro phosphorylation assay with mutagenesis and functional cellular readout\",\n      \"pmids\": [\"16488889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"NDR2 phosphorylates Rabin8 at Ser-272, which switches Rabin8 binding specificity from phosphatidylserine to Sec15 (exocyst component), thereby promoting Rab8 activation and ciliary membrane formation; loss of this phosphorylation impairs preciliary membrane assembly and ciliogenesis.\",\n      \"method\": \"In vitro kinase assay, phospho-mimetic and non-phosphorylatable Rabin8 mutants, ciliogenesis assay, lipid binding assay, Co-IP\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro phosphorylation plus mutagenesis plus functional ciliogenesis readout, multiple orthogonal methods\",\n      \"pmids\": [\"23435566\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Ndr2 phosphorylates β1-integrin at Thr-788/789 to stimulate PKC- and CaMKII-dependent β1-integrin activation and exocytosis; Ndr2 associates with integrin-positive early and recycling endosomes in hippocampal neurons; Ndr2 knockout mice show reduced surface expression of activated β1-integrins on dendrites and altered dendritic complexity in the hippocampus.\",\n      \"method\": \"In vitro phosphorylation assay, endosome fractionation, surface biotinylation, constitutive knockout mouse, immunofluorescence\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro kinase assay, subcellular fractionation, KO mouse with defined cellular phenotype\",\n      \"pmids\": [\"24719112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NDR2 localizes to peroxisomes via a C-terminal GKL sequence (PTS1-like motif) recognized by the PTS1 receptor Pex5p; this peroxisomal localization (absent in the NDR2-ΔL mutant lacking the C-terminal Leu) is required for NDR2's function in promoting primary ciliogenesis.\",\n      \"method\": \"Fluorescence microscopy colocalization with peroxisome markers, Pex5p binding assay, ciliogenesis rescue experiment with NDR2-ΔL mutant, PEX gene knockdown\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — receptor binding assay plus mutagenesis plus functional rescue experiment\",\n      \"pmids\": [\"28122914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Ndr2 becomes activated upon TCR stimulation and phosphorylates Filamin A (FLNa) at Ser-2152, promoting FLNa dissociation from LFA-1 and subsequent Talin/Kindlin-3 association that stabilizes the open (active) LFA-1 conformation in T cells.\",\n      \"method\": \"In vitro kinase assay, phospho-mimetic mutants, Co-IP, T-cell activation assays, LFA-1 conformation assay\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct in vitro phosphorylation with functional LFA-1 activation readout and Co-IP\",\n      \"pmids\": [\"30568657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NDR2 directly associates with both RIG-I and TRIM25, facilitating formation of the RIG-I/TRIM25 complex and enhancing TRIM25-mediated K63-linked polyubiquitination of RIG-I, which is required for RIG-I-mediated antiviral immune signaling; NDR2 conditional knockout mice show impaired antiviral responses.\",\n      \"method\": \"Co-IP, overexpression of kinase-inactive mutants, conditional knockout mice (Lysm+NDR2f/f), ubiquitination assay\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, ubiquitination assay, and conditional KO mouse with defined phenotype\",\n      \"pmids\": [\"30775439\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NDR2 directly interacts with GEF-H1 and phosphorylates it (at an NDR consensus motif HXRXXS/T), leading to RhoB GTPase inactivation; upon RASSF1A loss, this NDR2/GEF-H1/RhoB/YAP axis drives migration, metastasis, and cytokinesis defects in bronchial cells.\",\n      \"method\": \"Co-IP, siRNA/shRNA knockdown, phosphorylation assay, xenograft assay, genetic epistasis by sequential knockdown\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct Co-IP plus functional epistasis, single lab\",\n      \"pmids\": [\"30979377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"NDR2 interacts with E3 ubiquitin ligase Smurf1 and promotes Smurf1-mediated K48-linked ubiquitination of MEKK2, leading to MEKK2 degradation and inhibition of IL-17-induced inflammatory signaling.\",\n      \"method\": \"Co-IP, ubiquitination assay, siRNA knockdown, cytokine expression assays\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus ubiquitination assay, single lab\",\n      \"pmids\": [\"30504095\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NDR2 can be acetylated at K463; SIRT1 acts as the major deacetylase for NDR2, while p300 and CBP function as acetyltransferases; in SIRT1-deficient cells, HDAC6 and HDAC1/2 can deacetylate NDR2.\",\n      \"method\": \"Mass spectrometry identification of acetylation site, co-immunoprecipitation with acetyltransferases/deacetylases, SIRT1 knockout cell experiments\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP with functional deacetylase identification plus site-specific modification mapping\",\n      \"pmids\": [\"31427083\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM27 catalyzes K6- and K11-linked (non-degradative) ubiquitination of STK38L during starvation-induced autophagy, which promotes STK38L activation; activated STK38L then phosphorylates ULK1 at Ser-495, rendering ULK1 permissive for TRIM27-mediated K48-linked hyper-ubiquitination and proteasomal degradation, thereby restraining autophagy amplitude and duration.\",\n      \"method\": \"In vitro ubiquitination assay, in vitro kinase assay, Co-IP, site-directed mutagenesis, Trim27 knockout mice\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro ubiquitination and kinase assays, mutagenesis, KO mouse model, multiple orthogonal methods\",\n      \"pmids\": [\"35670107\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"STK38L (NDR2), induced by serum response factor (SRF) in response to lysophosphatidic acid (LPA), phosphorylates IRF3 at Ser-303, preventing IRF3 from proteasome-mediated degradation in the resting state, thereby maintaining sufficient IRF3 levels for rapid antiviral responses; STK38L-deficient mice show compromised innate antiviral responses.\",\n      \"method\": \"In vitro kinase assay, phospho-site mutagenesis, STK38L-knockout mice, IRF3 stability assay, viral challenge experiments\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct phosphorylation assay with mutagenesis, KO mouse with defined antiviral phenotype\",\n      \"pmids\": [\"36417850\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"STK38L depletion in KRAS-dependent PDAC cells (ADEX subtype) inhibits proliferation, induces apoptosis, and increases LATS2 kinase and p21 expression; LATS2 depletion partially rescues these effects, placing STK38L upstream of LATS2 in a pathway controlling PDAC cell viability.\",\n      \"method\": \"RNAi knockdown, genetic epistasis by double knockdown, apoptosis assay, cell proliferation assay\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis by double knockdown with defined cellular phenotype\",\n      \"pmids\": [\"29108249\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NDR2 (STK38L) promotes autophagy and mitophagy by mediating ULK1 instability, thereby acting as a negative regulator of osteoclastogenesis; myeloid-specific NDR2 knockout mice show lower bone mass and exacerbated bone loss, and ULK1 inhibition ameliorates the bone loss caused by NDR2 conditional knockout.\",\n      \"method\": \"Conditional knockout mice (Lysm+NDR2fl/fl), ULK1 stability assay, autophagy/mitophagy assays, ULK1 inhibitor rescue experiment\",\n      \"journal\": \"JCI insight\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO mouse with defined phenotype plus pharmacological rescue, single lab\",\n      \"pmids\": [\"39561008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SENP2 de-SUMOylates NDR2 at K463 (or nearby site), which improves NDR2 kinase activity; activated NDR2 then destabilizes p21, accelerating the G1/S cell cycle transition in lung cancer cells.\",\n      \"method\": \"Co-IP, SUMO deconjugation assay, kinase activity assay, cell cycle analysis, siRNA knockdown\",\n      \"journal\": \"European journal of pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical de-SUMOylation assay with functional kinase activity readout, single lab\",\n      \"pmids\": [\"38908669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NDR2 phosphorylates Rabin8 at S272 at the trans-Golgi/Golgi exit sites (GESs) to regulate Rab11-to-Rab8 succession; NDR2 interacts with VAMP7 at these sites; non-phosphorylatable Rabin8-S272A causes GES enlargement and disrupts rhodopsin Golgi-to-cilia trafficking in Xenopus rod photoreceptors.\",\n      \"method\": \"Transgenic Xenopus laevis expressing GFP-Rabin8 and phospho-mutants, Co-IP with VAMP7, fluorescence microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vivo phospho-mutant analysis in transgenic vertebrate photoreceptors with defined trafficking phenotype\",\n      \"pmids\": [\"39774853\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NDR2 regulates autophagosome formation and distribution in lung cancer cells in an ATG9A-dependent manner, and is required for lysosomal trafficking/fusion with autophagosomes; NDR2 silencing disrupts Golgi repositioning to the leading edge, inhibiting filopodia formation and cell migration under serum deprivation.\",\n      \"method\": \"siRNA/shRNA knockdown, LC3-II immunoblot, ATG9A functional assay, migration assay, Golgi repositioning microscopy, chloroquine block\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple functional assays in same cells, single lab\",\n      \"pmids\": [\"41390758\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NDR2 deficiency in hippocampal neurons reduces T788/789-phosphorylated β1-integrin at synaptic sites, decreases synaptic density, and reduces long-term potentiation in CA1 Schaffer collateral synapses; integrin-activating RGD peptide rescues LTP deficits, placing NDR2-mediated integrin phosphorylation upstream of synapse formation and plasticity.\",\n      \"method\": \"Constitutive NDR2 knockout mice, immunostaining for phospho-β1-integrin, synaptic density quantification, LTP electrophysiology, RGD peptide rescue\",\n      \"journal\": \"Journal of neurochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with electrophysiological and morphological phenotype plus pharmacological rescue, single lab\",\n      \"pmids\": [\"40439020\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"STK38L (NDR2) is a cytoplasmic serine/threonine kinase activated by multi-site phosphorylation (autophosphorylation at Ser-282, upstream kinase input at Thr-442) and by Mob protein binding, that localizes to peroxisomes via a C-terminal PTS1-like GKL motif and phosphorylates multiple substrates—including Rabin8 (Ser-272) to drive ciliogenesis, β1-integrin (Thr-788/789) to promote integrin trafficking and neurite/synapse development, Filamin A (Ser-2152) to initiate LFA-1 activation, ULK1 (Ser-495) to modulate autophagy, IRF3 (Ser-303) to maintain antiviral innate immune readiness, ARK5 (Thr-211) to support tumor cell survival, and GEF-H1 to regulate RhoB and cytokinesis—while its activity is further regulated by TRIM27-mediated ubiquitination, SENP2-mediated de-SUMOylation, and SIRT1/p300-mediated reversible acetylation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"STK38L (NDR2) is a cytoplasmic serine/threonine kinase of the NDR/LATS family that integrates phosphorylation, ubiquitination, SUMOylation, and acetylation inputs to regulate membrane trafficking, ciliogenesis, autophagy, integrin signaling, and innate immunity. Its catalytic activation requires autophosphorylation at Ser-282, upstream phosphorylation at Thr-442, and binding of Mob2 as an activating subunit, with additional regulation by TRIM27-mediated non-degradative ubiquitination, SENP2-mediated de-SUMOylation, and SIRT1/p300-controlled reversible acetylation at K463 [PMID:15037617, PMID:15067004, PMID:35670107, PMID:38908669, PMID:31427083]. STK38L phosphorylates Rabin8 at Ser-272 to drive Rab8 activation and ciliary membrane assembly from peroxisome-associated and Golgi exit sites, phosphorylates β1-integrin at Thr-788/789 to promote integrin trafficking and synaptic plasticity in hippocampal neurons, phosphorylates Filamin A at Ser-2152 to enable LFA-1 activation in T cells, and phosphorylates IRF3 at Ser-303 to stabilize IRF3 for antiviral innate immune responses [PMID:23435566, PMID:39774853, PMID:24719112, PMID:40439020, PMID:30568657, PMID:36417850]. STK38L also restrains autophagy amplitude by phosphorylating ULK1 at Ser-495, priming it for TRIM27-mediated degradation, scaffolds the RIG-I/TRIM25 complex to potentiate antiviral signaling, and promotes Smurf1-mediated degradation of MEKK2 to dampen IL-17-driven inflammation [PMID:35670107, PMID:39561008, PMID:30775439, PMID:30504095].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing the activation mechanism of NDR2 resolved how this kinase is switched on: Mob2 binding dramatically stimulates catalytic activity, while Ser-282 autophosphorylation and Thr-442 phosphorylation by an upstream kinase are both required, with S100B additionally stimulating autophosphorylation in vitro.\",\n      \"evidence\": \"Co-IP from Jurkat T-cells and HeLa cells with in vitro kinase assays, phospho-site mutagenesis, and okadaic acid treatment\",\n      \"pmids\": [\"15067004\", \"15037617\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The upstream kinase for Thr-442 was not definitively identified in these studies (PDK1 role was implied later)\",\n        \"How Mob2 binding allosterically activates NDR2 structurally is unresolved\",\n        \"Relative contributions of S100B vs. Mob2 in physiological contexts remain unclear\"\n      ]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Demonstrating that NDR2 is predominantly cytoplasmic and associates with the actin cytoskeleton in neurons established its distinct subcellular context compared to nuclear NDR1 and linked it to neurite morphology.\",\n      \"evidence\": \"Fluorescence microscopy of tagged proteins in HeLa/COS/PC12 cells and cortical neurons, actin co-precipitation\",\n      \"pmids\": [\"15037617\", \"15067004\", \"15308672\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether actin association is direct or scaffolded was not determined\",\n        \"Specific actin-binding domain not mapped\"\n      ]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Identifying ARK5 Thr-211 as a direct NDR2 substrate downstream of IGF-1 signaling was the first demonstration of NDR2 phosphorylating a defined substrate in a growth factor pathway relevant to cell survival and invasion.\",\n      \"evidence\": \"In vitro kinase assay with phospho-site mutagenesis, IGF-1 stimulation, cell survival and invasion assays\",\n      \"pmids\": [\"16488889\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether NDR2–ARK5 axis operates in non-cancer physiological contexts was not tested\",\n        \"PDK1 involvement at Thr-442 was suggested but not directly demonstrated with reconstituted components\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showing that NDR2 phosphorylates Rabin8 at Ser-272 to switch its binding from phosphatidylserine to the exocyst subunit Sec15, thereby activating Rab8 and driving ciliary membrane assembly, established NDR2 as a central regulator of ciliogenesis.\",\n      \"evidence\": \"In vitro kinase assay, phospho-mimetic/non-phosphorylatable Rabin8 mutants, lipid binding assay, ciliogenesis assay, Co-IP\",\n      \"pmids\": [\"23435566\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The upstream signal triggering NDR2 activation specifically for ciliogenesis was not identified\",\n        \"Whether other NDR family members can compensate was not addressed\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrating that Ndr2 phosphorylates β1-integrin at Thr-788/789 on endosomes and that Ndr2 knockout mice have reduced dendritic integrin activation and altered hippocampal morphology revealed a neuronal trafficking function for the kinase.\",\n      \"evidence\": \"In vitro phosphorylation, endosome fractionation, surface biotinylation, constitutive knockout mouse with hippocampal phenotype\",\n      \"pmids\": [\"24719112\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Which endosomal sorting machinery cooperates with NDR2-phosphorylated integrins was not defined\",\n        \"Behavioral consequences of altered dendritic complexity were not reported\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Localizing NDR2 to peroxisomes via its C-terminal PTS1-like GKL motif recognized by Pex5p, and showing this peroxisomal localization is required for ciliogenesis, linked peroxisome biology to ciliary membrane biogenesis through a single kinase.\",\n      \"evidence\": \"Colocalization with peroxisome markers, Pex5p binding assay, ciliogenesis rescue with NDR2-ΔL mutant, PEX gene knockdown\",\n      \"pmids\": [\"28122914\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How peroxisomal localization facilitates Rabin8 phosphorylation at ciliary precursor membranes is mechanistically unclear\",\n        \"Whether NDR2 has peroxisome-intrinsic substrates is unknown\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Placing STK38L upstream of LATS2 in KRAS-dependent pancreatic cancer cells, where its depletion induces apoptosis and p21 upregulation, identified a survival function in PDAC.\",\n      \"evidence\": \"RNAi epistasis by double knockdown of STK38L and LATS2, apoptosis and proliferation assays\",\n      \"pmids\": [\"29108249\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The direct biochemical mechanism linking STK38L to LATS2 regulation was not established\",\n        \"Generalizability beyond the ADEX PDAC subtype is untested\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identifying Filamin A Ser-2152 as a direct NDR2 substrate upon TCR stimulation, with phosphorylation releasing FLNa from LFA-1 to permit talin/kindlin-3 binding, revealed how NDR2 controls integrin inside-out activation in T cells.\",\n      \"evidence\": \"In vitro kinase assay, phospho-mimetic mutants, Co-IP, LFA-1 conformation assay in T cells\",\n      \"pmids\": [\"30568657\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How TCR signaling activates NDR2 was not defined\",\n        \"Whether this mechanism operates for integrins beyond LFA-1 is unknown\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrating that NDR2 scaffolds Smurf1-mediated K48-ubiquitination and degradation of MEKK2 to suppress IL-17 inflammatory signaling extended NDR2 function to a kinase-independent scaffolding role in innate inflammation.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, siRNA knockdown, cytokine expression\",\n      \"pmids\": [\"30504095\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether NDR2 kinase activity is required for the Smurf1 interaction was not tested\",\n        \"Independent replication needed\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showing that NDR2 bridges RIG-I and TRIM25 to enhance K63-polyubiquitination of RIG-I, with conditional knockout mice displaying impaired antiviral responses, established a scaffolding function in innate antiviral immunity.\",\n      \"evidence\": \"Co-IP, kinase-inactive mutants, ubiquitination assay, Lysm-Cre conditional KO mice with viral challenge\",\n      \"pmids\": [\"30775439\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether kinase activity or only scaffolding is needed for RIG-I activation was not fully resolved\",\n        \"Contribution relative to NDR1 in the same pathway not addressed\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identifying GEF-H1 as a direct NDR2 substrate whose phosphorylation inactivates RhoB, driving a RASSF1A-loss-dependent migration and cytokinesis defect axis, connected NDR2 to Rho GTPase regulation in cancer.\",\n      \"evidence\": \"Co-IP, phosphorylation assay, siRNA epistasis, xenograft assay\",\n      \"pmids\": [\"30979377\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The exact phosphorylation site on GEF-H1 was not fully mapped\",\n        \"Independent validation in non-bronchial cell types is lacking\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Mapping reversible acetylation of NDR2 at K463 controlled by SIRT1 (deacetylase) and p300/CBP (acetyltransferases) added a post-translational regulatory layer, with HDAC6 and HDAC1/2 serving as backup deacetylases in SIRT1-deficient cells.\",\n      \"evidence\": \"Mass spectrometry, Co-IP with acetyltransferases/deacetylases, SIRT1 KO cells\",\n      \"pmids\": [\"31427083\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of acetylation on kinase activity or substrate selection was not determined\",\n        \"Whether K463 acetylation and SUMOylation compete at the same residue was not tested\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrating that TRIM27 non-degradatively ubiquitinates STK38L (K6/K11 chains) to activate it, after which STK38L phosphorylates ULK1 at Ser-495 to prime ULK1 for TRIM27-mediated K48-ubiquitination and degradation, revealed a feedback circuit that restrains autophagy amplitude.\",\n      \"evidence\": \"In vitro ubiquitination and kinase assays, mutagenesis, Co-IP, Trim27 KO mice\",\n      \"pmids\": [\"35670107\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether TRIM27-mediated ubiquitination of STK38L is stimulus-specific beyond starvation is unknown\",\n        \"The deubiquitinase counteracting TRIM27 on STK38L was not identified\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identifying IRF3 Ser-303 as a direct STK38L substrate that prevents IRF3 proteasomal degradation at steady state, with STK38L-KO mice showing compromised antiviral responses, established STK38L as a constitutive guardian of innate immune readiness.\",\n      \"evidence\": \"In vitro kinase assay, phospho-site mutagenesis, STK38L-KO mice with viral challenge, IRF3 stability assay\",\n      \"pmids\": [\"36417850\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The proteasomal pathway that degrades unphosphorylated IRF3 was not identified\",\n        \"Whether NDR1 can partially compensate for IRF3 stabilization is untested\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealing that SENP2-mediated de-SUMOylation at K463 enhances NDR2 kinase activity, which then destabilizes p21 to accelerate G1/S transition, added SUMOylation as a regulatory switch converging on the same residue as acetylation.\",\n      \"evidence\": \"SUMO deconjugation assay, kinase activity assay, cell cycle analysis, siRNA in lung cancer cells\",\n      \"pmids\": [\"38908669\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The SUMO E3 ligase responsible for NDR2 SUMOylation was not identified\",\n        \"Interplay between SUMOylation, acetylation, and ubiquitination at K463 needs systematic analysis\",\n        \"Independent replication outside lung cancer cells is lacking\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Conditional myeloid NDR2 knockout mice showing lower bone mass due to enhanced osteoclastogenesis, rescued by ULK1 inhibition, connected the NDR2–ULK1 autophagy axis to bone homeostasis in vivo.\",\n      \"evidence\": \"Lysm-Cre conditional KO mice, autophagy/mitophagy assays, ULK1 inhibitor rescue\",\n      \"pmids\": [\"39561008\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether NDR2 directly phosphorylates ULK1 in osteoclast precursors or acts through TRIM27 was not tested\",\n        \"Single-lab finding awaiting independent replication\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showing NDR2 phosphorylates Rabin8 at S272 at trans-Golgi/Golgi exit sites in vertebrate photoreceptors, interacts with VAMP7, and is required for rhodopsin Golgi-to-cilia trafficking extended the Rabin8 phosphorylation mechanism to specialized sensory cilia in vivo.\",\n      \"evidence\": \"Transgenic Xenopus expressing GFP-Rabin8 phospho-mutants, Co-IP with VAMP7, fluorescence microscopy of rod photoreceptors\",\n      \"pmids\": [\"39774853\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether NDR2 directly binds VAMP7 or is scaffolded remains unclear\",\n        \"Mammalian photoreceptor validation not yet shown\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrating that NDR2 deficiency in hippocampal neurons reduces phospho-β1-integrin at synapses, decreases synaptic density, and impairs LTP — rescued by integrin-activating RGD peptide — established NDR2 as essential for synapse formation and plasticity via integrin signaling.\",\n      \"evidence\": \"Constitutive NDR2 KO mice, phospho-β1-integrin immunostaining, synaptic density quantification, LTP electrophysiology, RGD peptide rescue\",\n      \"pmids\": [\"40439020\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Behavioral consequences (learning/memory) in NDR2 KO mice not reported\",\n        \"Whether NDR2 acts cell-autonomously in postsynaptic neurons vs. presynaptic was not dissected\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linking NDR2 to ATG9A-dependent autophagosome formation, lysosomal trafficking, and Golgi repositioning for filopodia-driven migration in lung cancer cells added a migration-autophagy nexus to NDR2 function.\",\n      \"evidence\": \"siRNA/shRNA knockdown, LC3-II immunoblot, ATG9A functional assay, migration assay, Golgi repositioning microscopy\",\n      \"pmids\": [\"41390758\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct substrate linking NDR2 to ATG9A regulation not identified\",\n        \"Relationship to the TRIM27–ULK1 axis not tested\",\n        \"Single-lab finding in cancer cell lines\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the diverse post-translational modifications of STK38L at K463 (acetylation, SUMOylation) and elsewhere (ubiquitination, phosphorylation) are temporally coordinated to direct substrate selection across its multiple functions — ciliogenesis, autophagy, integrin trafficking, and innate immunity — remains an open question.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of NDR2 with Mob2 or substrates is available\",\n        \"Systematic identification of the full substrate repertoire has not been performed\",\n        \"Relative contributions of NDR1 vs. NDR2 to shared pathways are poorly defined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 5, 6, 7, 9, 11, 14, 15, 19]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [10, 12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005777\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [19]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [5, 7, 9, 11, 16]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [10, 12, 15]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [14, 17, 20]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [6, 8, 19]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [18]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [7, 21]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"MOB2\",\n      \"TRIM27\",\n      \"RAB3IP\",\n      \"ITGB1\",\n      \"FLNA\",\n      \"IRF3\",\n      \"ULK1\",\n      \"ARHGEF2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}