{"gene":"PDLIM1","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2000,"finding":"CLP-36 (PDLIM1) localizes to actin stress fibers in nonmuscle cells via its PDZ domain, which associates with the spectrin-like repeats of alpha-actinin. Both nonmuscle alpha-actinin-1 and alpha-actinin-4 form complexes with CLP-36, as demonstrated by immunoprecipitation and MALDI-TOF mass spectrometry.","method":"Co-immunoprecipitation, MALDI-TOF MS, subcellular localization by fluorescence microscopy, domain deletion analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP with MS confirmation, domain-mapping experiments, replicated across two isoforms and independently confirmed in a second paper (PMID:11110697)","pmids":["10753915"],"is_preprint":false},{"year":2000,"finding":"Human CLP36 (PDLIM1) binds alpha-actinin-1 via its intervening sequence (not the PDZ or LIM domain alone), as shown by yeast two-hybrid analysis mapping to spectrin-like repeats 2 and 3 of alpha-actinin-1. CLP36 associates with actin filaments and stress fibers in activated platelets and endothelial cells and is absent from focal adhesions. The N-terminal PDZ domain plus intervening region, but not the LIM domain alone, targets CLP36 to stress fibers.","method":"Co-immunoprecipitation, pull-down assays, yeast two-hybrid, blot overlay, GFP fusion localization in endothelial cells","journal":"Blood","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (Co-IP, pulldown, Y2H, blot overlay, domain deletion + GFP targeting), single lab with rigorous controls","pmids":["11110697"],"is_preprint":false},{"year":2000,"finding":"hCLIM1 (PDLIM1) interacts with alpha-actinin-2 (skeletal muscle isoform) via its LIM domain binding to the EF-hand region of alpha-actinin-2, defining a new mode of LIM domain interaction. hCLIM1 colocalizes with alpha-actinin at Z-disks in human myocardium.","method":"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence colocalization","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Y2H domain mapping plus Co-IP in a single lab, two orthogonal methods","pmids":["10861853"],"is_preprint":false},{"year":2002,"finding":"CLP-36 (PDLIM1) acts as an adapter that recruits the novel kinase Clik1 to actin stress fibers via its C-terminal LIM domain. Clik1 is otherwise predominantly nuclear; association with CLP-36 relocalizes it to actin stress fibers, where it disrupts the periodic staining pattern of CLP-36.","method":"Yeast two-hybrid, subcellular colocalization, domain deletion analysis","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Y2H interaction mapping plus functional relocalization experiment, single lab","pmids":["11973348"],"is_preprint":false},{"year":2007,"finding":"CLP36 (PDLIM1) is required for actin stress fiber formation and focal adhesion assembly in BeWo cells. RNAi-mediated knockdown caused loss of stress fibers and focal adhesions; rescue required both the PDZ and LIM domains, establishing that both domains are functionally essential.","method":"RNAi knockdown, rescue with domain-deletion mutants, fluorescence microscopy","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with defined phenotype plus domain-mutation rescue, single lab","pmids":["17964547"],"is_preprint":false},{"year":2007,"finding":"PDLIM1 (CLP36) is the PDZ domain-containing protein that tethers Plasma Membrane Ca2+-ATPase (PMCA) to the cytoskeleton in resting platelets via PDZ domain interactions with the C-terminal PDZ-binding motif of PMCA4b. CLP36, PMCA, alpha-actinin, and actin co-elute as a ~1,000 kDa complex by gel filtration, and CLP36 colocalizes with PMCA in both resting and activated platelets.","method":"Co-immunoprecipitation, LC-MS/MS, GST pull-down, gel filtration chromatography, immunofluorescence microscopy","journal":"Thrombosis and haemostasis","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, MS, GST pulldown, gel filtration, colocalization) in single study with rigorous controls","pmids":["17393022"],"is_preprint":false},{"year":2009,"finding":"CLP36 (PDLIM1) interacts with palladin via its PDZ domain binding to the C-terminus of palladin. Palladin silencing suppresses CLP36 localization to stress fibers, and overexpression of the PDZ domain alone inhibits palladin localization to stress fibers. Alpha-actinin, CLP36, and palladin form a protein complex important for actin cytoskeleton regulation.","method":"Yeast two-hybrid, co-immunoprecipitation, siRNA knockdown, overexpression of domain constructs, fluorescence microscopy","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Y2H plus Co-IP plus functional knockdown, single lab","pmids":["19366376"],"is_preprint":false},{"year":2009,"finding":"CLP36 (PDLIM1) forms a complex with alpha-actinin in sensory (DRG) neurons, localizes to actin cytoskeleton in growth cones, and negatively regulates neurite outgrowth: RNAi knockdown of CLP36 induced lamellipodia and increased neurite length and number, whereas overexpression of the PDZ domain alone perturbed neurite outgrowth.","method":"RNAi, overexpression of deletion mutants, fluorescence microscopy, co-immunoprecipitation","journal":"Journal of neurochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with defined morphological phenotype plus domain overexpression, single lab","pmids":["19780892"],"is_preprint":false},{"year":2010,"finding":"CLP36 (PDLIM1) interacts with palladin in dorsal root ganglion neurons, forming a complex detectable by co-immunoprecipitation; both proteins colocalize in neurites and cell bodies of primary DRG neurons. Sciatic nerve transection upregulates both CLP36 and palladin mRNAs, with CLP36 being more prominently upregulated, suggesting a specific role in nerve regeneration.","method":"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence, qRT-PCR after nerve injury","journal":"Neuroscience letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Y2H plus Co-IP in primary neurons, single lab","pmids":["20381583"],"is_preprint":false},{"year":2011,"finding":"Alpha-actinin-4 and CLP36 (PDLIM1) form a complex in normal podocytes. siRNA depletion of alpha-actinin-4 markedly reduces CLP36 protein levels. FSGS-associated alpha-actinin-4 mutations (R310Q, Q348R) inhibit complex formation between alpha-actinin-4 and CLP36. Disruption of the alpha-actinin-4–CLP36 complex or reduction of CLP36 significantly inhibits RhoA activity and traction force generation in podocytes.","method":"Co-immunoprecipitation, siRNA knockdown, mutant overexpression, RhoA activity assay, traction force microscopy","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, siRNA, disease-mutant functional analysis, RhoA assay, traction force), single lab with rigorous controls","pmids":["21680739"],"is_preprint":false},{"year":2011,"finding":"PDLIM1 exists as part of a complex with FHL1, ACTN1, GSN (gelsolin), and ACTN4, identified by tandem affinity purification from HEK-293 cells and verified by co-immunoprecipitation from mouse heart ventricles and 3D fluorescence microscopy in adult cardiomyocytes.","method":"Tandem affinity purification, LC-MS, co-immunoprecipitation, 3D fluorescence microscopy","journal":"Molecular bioSystems","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — TAP-MS plus reciprocal Co-IP verification in native tissue, single lab","pmids":["21246116"],"is_preprint":false},{"year":2012,"finding":"The LIM domain of PDLIM1 binds two zinc ions with femtomolar affinity (Kd avg ~2.5×10⁻¹⁴ M), and protein-protein interactions with the C-terminal extension further elevate Zn2+ affinity. Domain stability depends not only on zinc coordination but significantly on protein-protein interactions involving the C-terminus.","method":"Thermal denaturation, mass spectrometry, limited proteolysis, circular dichroism, zinc affinity measurements","journal":"Journal of inorganic biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple biophysical and biochemical methods characterizing intrinsic biochemical properties in vitro, single lab but comprehensive","pmids":["22922308"],"is_preprint":false},{"year":2012,"finding":"CLP36 (PDLIM1) acts as a major inhibitor of GPVI/ITAM signaling in platelets. Mice expressing truncated CLP36 lacking the LIM domain or CLP36 knockout mice displayed hyperactivation (hyperphosphorylation, enhanced Ca2+ mobilization, granule secretion, integrin activation) specifically downstream of GPVI, leading to accelerated thrombus formation in vivo.","method":"Genetic knockout and truncation mouse models, platelet functional assays (Ca2+ mobilization, integrin activation, granule secretion), in vivo thrombosis models, phosphoprotein analysis","journal":"Circulation research","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO plus domain-truncation mouse models with multiple functional readouts and in vivo validation, rigorous controls","pmids":["22955732"],"is_preprint":false},{"year":2012,"finding":"CLP36 and RIL (another ALP/Enigma family member) form a complex with alpha-actinin-1 and palladin on stress fibers. CLP36 depletion in F2408 fibroblasts caused non-oriented stress fiber organization; RIL compensated for this role. CLP36 and RIL have redundant roles in stress fiber formation but distinct effects on stress fiber dynamics.","method":"RNAi knockdown, time-lapse microscopy, co-immunoprecipitation, fluorescence microscopy","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with defined phenotype plus Co-IP complex verification, single lab","pmids":["22659164"],"is_preprint":false},{"year":2014,"finding":"CLP36 (PDLIM1) promotes breast cancer cell migration and invasion through interaction with alpha-actinin-1 and alpha-actinin-4. Mutations abolishing alpha-actinin-binding activity eliminated the ability of CLP36 to promote migration. CLP36 depletion or disruption of the CLP36–alpha-actinin complex substantially inhibited Cdc42 activation, cell polarization, and directional migration.","method":"Co-immunoprecipitation, siRNA knockdown, binding-interface mutagenesis, Cdc42 GTPase activity assay, migration/invasion assays, in vivo metastasis model","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, mutagenesis of binding interface, Cdc42 activity assay, in vivo validation; multiple orthogonal methods in single study","pmids":["24662836"],"is_preprint":false},{"year":2015,"finding":"PDLIM1 interacts with and stabilizes the E-cadherin/β-catenin complex at cell-cell junctions, thereby inhibiting β-catenin nuclear translocation and transcriptional activity and suppressing EMT in colorectal cancer cells. PDLIM1 knockdown increased nuclear β-catenin activity and promoted invasion, while overexpression attenuated EMT.","method":"Co-immunoprecipitation, siRNA knockdown, overexpression, β-catenin reporter assay, in vivo orthotopic and lung metastasis mouse models","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP interaction, reporter assay for β-catenin activity, KD/OE with defined EMT phenotype, in vivo validation; multiple orthogonal methods","pmids":["26701804"],"is_preprint":false},{"year":2015,"finding":"PDLIM1 inhibits NF-κB-mediated inflammatory signaling by sequestering the p65 subunit of NF-κB in the cytoplasm in an IκBα-independent but alpha-actinin-4-dependent manner. PDLIM1 deficiency leads to increased nuclear p65 levels and enhanced proinflammatory cytokine production in response to innate stimuli.","method":"Co-immunoprecipitation, siRNA knockdown, subcellular fractionation, nuclear p65 quantification, cytokine ELISA","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, subcellular fractionation, KD with cytokine readout; single lab, multiple methods","pmids":["26679095"],"is_preprint":false},{"year":2015,"finding":"PDLIM1 interacts with the neurotrophin receptor p75NTR (CD271) via its PDZ domain binding to the C-terminal SPV PDZ-binding motif of p75NTR. This interaction is regulated by S425 phosphorylation of p75NTR. The interaction also requires that p75NTR not be phosphorylated at S303 by PKA. shRNA knockdown of PDLIM1 completely ablated p75NTR-mediated glioma invasion in vitro and in vivo.","method":"Peptide-based interaction screen, co-immunoprecipitation, phosphorylation mutant analysis, shRNA knockdown, in vivo glioma invasion model","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with phosphomutant dissection plus in vivo shRNA validation, single lab","pmids":["26119933"],"is_preprint":false},{"year":2016,"finding":"PDLIM1 must be degraded via the autophagy-lysosome pathway (dependent on ATG7) to allow proper cytoskeletal reorganization during spermatid differentiation. In atg7-null mice, PDLIM1 accumulates, impairing cytoskeleton organization and leading to defects in flagella biogenesis and cytoplasm removal during spermiogenesis.","method":"Conditional knockout mouse model (atg7-null), functional screening, western blot, phenotypic analysis of sperm morphology and motility","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with defined phenotypic readout linking PDLIM1 accumulation to cytoskeletal defects, single lab","pmids":["27310465"],"is_preprint":false},{"year":2020,"finding":"PDLIM1 competitively binds alpha-actinin-4 (ACTN4), leading to dissociation of ACTN4 from F-actin and preventing F-actin overgrowth. Loss of PDLIM1 induces excessive F-actin formation, resulting in dephosphorylation of LATS1 and activation of YAP, promoting HCC metastasis via the Hippo pathway. Asn145 (N145) of PDLIM1 is critical for its interaction with ACTN4, and N145A mutation abolishes this regulatory function.","method":"Co-immunoprecipitation, site-directed mutagenesis (N145A), F-actin binding assay, LATS1 phosphorylation assay, YAP activity measurement, in vitro invasion and in vivo metastasis models","journal":"Hepatology (Baltimore, Md.)","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — mutagenesis identifying critical residue, Co-IP, F-actin assays, Hippo pathway signaling readout, in vivo validation; multiple orthogonal methods","pmids":["31509262"],"is_preprint":false},{"year":2020,"finding":"PDLIM1 localizes to actin-rich structures generated by bacterial pathogens: it accumulates at sites of Listeria entry, in actin clouds surrounding immotile bacteria, and within actin comet/rocket tails. PDLIM1 is maintained in the actin core of membrane protrusions but absent from the membrane invagination internalizing Listeria. PDLIM1 is also a component of EPEC pedestals and its recruitment is dependent on the bacterial effector Tir.","method":"Immunofluorescence microscopy, subcellular localization during bacterial infection, Tir-deletion bacterial mutant analysis","journal":"Anatomical record (Hoboken, N.J. : 2007)","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiments with mechanistic dissection (Tir-dependence), single lab","pmids":["33022122"],"is_preprint":false},{"year":2022,"finding":"CLP36 (PDLIM1) promotes p53-deficient sarcoma progression by inhibiting AIP-4 (ITCH E3 ligase)-dependent proteasomal degradation of YAP1, thereby increasing YAP1 protein levels. CLP36 knockout in mice markedly inhibited p53-deficiency-induced tumorigenesis.","method":"Co-immunoprecipitation, genetic KO mouse model, ubiquitination assay, western blot, tumor growth assay","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, in vivo KO model; single lab with multiple methods","pmids":["35836803"],"is_preprint":false},{"year":2023,"finding":"PDLIM1 interacts with hexokinase 2 (HK2) in gastric cancer cells, as demonstrated by co-immunoprecipitation. This interaction mediates glycolysis and cell biological behaviors under glucose deprivation through the Wnt/β-catenin signaling pathway.","method":"Co-immunoprecipitation, glucose metabolism assays (glycolytic indicators), western blot, siRNA knockdown and overexpression","journal":"Cell and tissue research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP in a single lab with limited mechanistic follow-up","pmids":["37930472"],"is_preprint":false},{"year":2025,"finding":"Cblb (an E3 ubiquitin ligase) binds to the PDZ and LIM domains of PDLIM1 and ubiquitinates PDLIM1 at K244, targeting it for proteasome-mediated degradation. In microglia, this Cblb-mediated degradation of PDLIM1 releases NF-κB signaling, promoting pyroptosis. Botulinum toxin A suppresses Cblb activity, thereby preventing PDLIM1 degradation and inhibiting NF-κB-mediated pyroptosis.","method":"Mass spectrometry, co-immunoprecipitation, ubiquitination assay (K244 site identification), proteasome inhibition, shRNA knockdown, lentiviral/AAV rescue experiments in vivo","journal":"The journal of headache and pain","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS identification + Co-IP + site-specific ubiquitination mapping + in vivo rescue, single lab","pmids":["40696327"],"is_preprint":false}],"current_model":"PDLIM1 (CLP-36/hCLIM1) is a scaffold/adapter protein that localizes to actin stress fibers in nonmuscle cells by binding alpha-actinin isoforms (ACTN1, ACTN4) via its PDZ domain and intervening sequence; it recruits binding partners (including the Clik1 kinase and palladin) to actin structures via its LIM domain, regulates F-actin dynamics by competing with ACTN4 for actin binding to control Hippo/LATS1/YAP signaling, sequesters NF-κB p65 in the cytoplasm in an alpha-actinin-4-dependent manner to suppress inflammation, stabilizes the E-cadherin/β-catenin junctional complex to inhibit EMT, and is subject to proteasomal degradation through Cblb-mediated K244 ubiquitination as well as autophagy-lysosome-dependent degradation during spermatogenesis."},"narrative":{"mechanistic_narrative":"PDLIM1 (CLP-36/hCLIM1) is a PDZ-LIM scaffold protein that organizes the actin cytoskeleton and couples it to signaling by tethering alpha-actinin and its associated partners onto actin stress fibers [PMID:10753915, PMID:11110697]. Its bipartite architecture underlies this adapter role: the N-terminal PDZ domain plus an intervening sequence binds the spectrin-like repeats of nonmuscle alpha-actinin-1 and alpha-actinin-4 and targets the protein to stress fibers (while the LIM domain alone does not), and the C-terminal LIM domain recruits additional clients such as the Clik1 kinase to those actin structures [PMID:10753915, PMID:11110697, PMID:11973348]. Through these interactions PDLIM1 builds higher-order complexes with palladin and other actin regulators and is itself required for stress fiber and focal adhesion assembly [PMID:17964547, PMID:19366376, PMID:22659164]. Beyond structural scaffolding, PDLIM1 controls Rho-family and Hippo signaling at the actin interface: the alpha-actinin-4 complex governs RhoA activity and traction force generation [PMID:21680739], the alpha-actinin complex drives Cdc42 activation and directional cell migration [PMID:24662836], and competitive binding of alpha-actinin-4 to limit F-actin overgrowth restrains LATS1 dephosphorylation and YAP activation [PMID:31509262]. PDLIM1 additionally functions as a cytoplasmic sequestering hub for transcription factors, retaining NF-kB p65 in the cytoplasm in an alpha-actinin-4-dependent manner to suppress inflammation [PMID:26679095] and stabilizing the E-cadherin/beta-catenin junctional complex to block beta-catenin nuclear activity and EMT [PMID:26701804]. PDLIM1 abundance is set by regulated degradation, including Cblb-mediated K244 ubiquitination and proteasomal turnover that releases NF-kB-driven pyroptosis [PMID:40696327] and ATG7-dependent autophagic clearance required for cytoskeletal remodeling during spermiogenesis [PMID:27310465]. In platelets, PDLIM1 acts as a major negative regulator of GPVI/ITAM signaling, limiting thrombus formation [PMID:22955732].","teleology":[{"year":2000,"claim":"Established the founding function of PDLIM1 as a stress-fiber adapter, defining how a PDZ-LIM protein is targeted to the actin cytoskeleton through alpha-actinin binding.","evidence":"Co-IP with MALDI-TOF MS, yeast two-hybrid domain mapping, and GFP-fusion localization in nonmuscle, endothelial, and platelet cells","pmids":["10753915","11110697","10861853"],"confidence":"High","gaps":["Did not establish whether actin association is direct or fully alpha-actinin-mediated","Functional consequence of stress-fiber targeting not yet tested"]},{"year":2002,"claim":"Showed PDLIM1 is not just a structural anchor but recruits signaling enzymes to actin, redistributing the otherwise nuclear Clik1 kinase to stress fibers via its LIM domain.","evidence":"Yeast two-hybrid and colocalization with domain-deletion analysis","pmids":["11973348"],"confidence":"Medium","gaps":["Clik1 substrates on stress fibers unidentified","Functional output of LIM-mediated kinase recruitment untested"]},{"year":2007,"claim":"Demonstrated PDLIM1 is functionally required, not merely associated, for actin stress fiber and focal adhesion assembly, and that both PDZ and LIM domains are essential.","evidence":"RNAi knockdown with domain-deletion rescue in BeWo cells","pmids":["17964547"],"confidence":"Medium","gaps":["Molecular step in assembly that PDLIM1 controls unresolved","Cell-type generality of the requirement not established here"]},{"year":2007,"claim":"Extended the scaffold concept to membrane-cytoskeleton coupling by showing PDLIM1 tethers the PMCA calcium pump to the actin/alpha-actinin network in platelets.","evidence":"Co-IP, LC-MS/MS, GST pulldown, gel filtration of a ~1,000 kDa complex, and colocalization","pmids":["17393022"],"confidence":"High","gaps":["Functional consequence for calcium handling not directly measured","Stoichiometry of the megacomplex undefined"]},{"year":2009,"claim":"Identified palladin as a PDZ-domain partner and placed PDLIM1 in an alpha-actinin/palladin complex with mutual dependence for stress-fiber localization, including in neurons where PDLIM1 negatively regulates neurite outgrowth.","evidence":"Y2H, Co-IP, siRNA, and domain-overexpression microscopy in fibroblasts and DRG neurons","pmids":["19366376","19780892","20381583"],"confidence":"Medium","gaps":["Signaling pathway linking the complex to outgrowth suppression unknown","Relevance of nerve-injury upregulation to regeneration not functionally tested"]},{"year":2011,"claim":"Linked the PDLIM1/alpha-actinin-4 complex to active cytoskeletal mechanics and disease, showing it controls RhoA activity and traction force and is disrupted by FSGS-causing alpha-actinin-4 mutations.","evidence":"Co-IP, siRNA, disease-mutant analysis, RhoA assay, and traction force microscopy in podocytes; TAP-MS complex definition in cardiac tissue","pmids":["21680739","21246116"],"confidence":"High","gaps":["Mechanism by which the complex regulates RhoA not defined","Whether reduced PDLIM1 levels are cause or consequence of complex loss unclear"]},{"year":2012,"claim":"Defined PDLIM1's intrinsic biochemistry (femtomolar dual-zinc LIM domain stabilized by C-terminal interactions) and revealed a genetically validated negative-regulatory role in platelet GPVI/ITAM signaling and thrombosis.","evidence":"Biophysical zinc-affinity measurements in vitro; knockout and LIM-truncation mouse models with platelet functional assays and in vivo thrombosis; plus redundancy analysis with RIL on stress fibers","pmids":["22922308","22955732","22659164"],"confidence":"High","gaps":["Molecular target of PDLIM1 in the GPVI cascade not identified","Extent of functional redundancy with other ALP/Enigma members in vivo unknown"]},{"year":2014,"claim":"Established PDLIM1 as a pro-migratory effector in cancer that drives Cdc42 activation, cell polarization, and metastasis strictly through its alpha-actinin interaction.","evidence":"Binding-interface mutagenesis, Cdc42 activity assay, migration/invasion assays, and in vivo metastasis in breast cancer cells","pmids":["24662836"],"confidence":"High","gaps":["Link from the actin complex to Cdc42 GEF/GAP regulation undefined","Context-dependence versus tumor-suppressive roles in other cancers unreconciled"]},{"year":2015,"claim":"Revealed PDLIM1 as a cytoplasmic sequestering hub controlling transcription-factor localization—stabilizing E-cadherin/beta-catenin junctions to block EMT and retaining NF-kB p65 in the cytoplasm to suppress inflammation.","evidence":"Co-IP, knockdown/overexpression, reporter assays, subcellular fractionation, cytokine ELISA, and in vivo metastasis models; plus PDZ-mediated p75NTR binding driving glioma invasion","pmids":["26701804","26679095","26119933"],"confidence":"High","gaps":["How a single scaffold reconciles tumor-suppressive (EMT/NF-kB) and tumor-promoting (p75NTR) outputs unresolved","Whether p65 sequestration is direct or alpha-actinin-4-bridged not fully dissected"]},{"year":2016,"claim":"Showed PDLIM1 abundance must be actively lowered for cytoskeletal remodeling, with ATG7-dependent autophagic degradation required during spermatid differentiation.","evidence":"atg7-null conditional knockout mice with western blot and sperm morphology/motility phenotyping","pmids":["27310465"],"confidence":"Medium","gaps":["Autophagy receptor selecting PDLIM1 unidentified","Whether PDLIM1 accumulation is sufficient to cause the spermiogenesis defect not isolated"]},{"year":2020,"claim":"Provided a mechanistic link from PDLIM1 to Hippo signaling, showing competitive sequestration of alpha-actinin-4 from F-actin (via residue N145) limits F-actin overgrowth, preserving LATS1 phosphorylation and restraining YAP-driven HCC metastasis; also placed PDLIM1 at pathogen-induced actin structures.","evidence":"N145A mutagenesis, Co-IP, F-actin binding and LATS1 phosphorylation/YAP assays with in vivo metastasis; immunofluorescence at Listeria/EPEC actin structures with Tir-mutant analysis","pmids":["31509262","33022122"],"confidence":"High","gaps":["How F-actin level changes are transduced to the LATS1 kinase cassette not detailed","Functional role of PDLIM1 at bacterial actin structures untested"]},{"year":2022,"claim":"Identified a second, opposing route by which PDLIM1 controls YAP—protecting YAP1 from ITCH/AIP-4-dependent proteasomal degradation to promote p53-deficient sarcoma.","evidence":"Co-IP, ubiquitination assay, and CLP36-knockout mouse tumorigenesis model","pmids":["35836803"],"confidence":"Medium","gaps":["How PDLIM1 shields YAP1 from ITCH mechanistically unclear","Reconciliation with the F-actin/LATS1 route to YAP regulation not addressed"]},{"year":2023,"claim":"Suggested a metabolic interaction in which PDLIM1 binds hexokinase 2 to influence glycolysis under glucose deprivation via Wnt/beta-catenin signaling.","evidence":"Single Co-IP with glycolysis assays and knockdown/overexpression in gastric cancer cells","pmids":["37930472"],"confidence":"Low","gaps":["Single Co-IP without reciprocal or orthogonal validation","Direct versus indirect HK2 association undetermined","Mechanistic link to Wnt/beta-catenin not established"]},{"year":2025,"claim":"Defined how PDLIM1 protein levels are set by the ubiquitin-proteasome system, identifying Cblb as the E3 ligase ubiquitinating K244, with degradation releasing NF-kB-driven microglial pyroptosis.","evidence":"Mass spectrometry, Co-IP, K244 site-specific ubiquitination mapping, proteasome inhibition, and in vivo shRNA/AAV rescue","pmids":["40696327"],"confidence":"Medium","gaps":["Signals controlling Cblb-PDLIM1 engagement unknown","Whether NF-kB release reflects loss of p65 sequestration not directly connected to the 2015 mechanism"]},{"year":null,"claim":"How PDLIM1 toggles between tumor-suppressive (E-cadherin/beta-catenin stabilization, NF-kB sequestration, F-actin/LATS1-mediated YAP restraint) and tumor-promoting (Cdc42 migration, YAP1 stabilization, p75NTR invasion) outputs remains the central unresolved question.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model reconciling opposing context-dependent roles","Structural basis distinguishing competing partner-selection states unknown","Upstream signals dictating which complex PDLIM1 forms not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,3,6,5]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,1,4,13,19]},{"term_id":"GO:0140313","term_label":"molecular sequestering activity","supporting_discovery_ids":[15,16]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[9,14,19,12]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,1,4,13,7]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[15,16]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[19,9,14,16]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[9,15,19,21]},{"term_id":"R-HSA-109582","term_label":"Hemostasis","supporting_discovery_ids":[5,12]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[16,23]}],"complexes":["PDLIM1/alpha-actinin/palladin actin stress-fiber complex","PDLIM1/PMCA4b/alpha-actinin/actin platelet complex","E-cadherin/beta-catenin junctional complex"],"partners":["ACTN1","ACTN4","ACTN2","PALLD","CLIK1","P65/RELA","YAP1","CBLB"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O00151","full_name":"PDZ and LIM domain protein 1","aliases":["C-terminal LIM domain protein 1","Elfin","LIM domain protein CLP-36"],"length_aa":329,"mass_kda":36.1,"function":"Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton (PubMed:10861853). Involved in assembly, disassembly and directioning of stress fibers in fibroblasts. Required for the localization of ACTN1 and PALLD to stress fibers. Required for cell migration and in maintaining cell polarity of fibroblasts (By similarity)","subcellular_location":"Cytoplasm; Cytoplasm, cytoskeleton; Cytoplasm, myofibril, sarcomere, Z line","url":"https://www.uniprot.org/uniprotkb/O00151/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PDLIM1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ACTN4","stoichiometry":0.2},{"gene":"RANBP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PDLIM1","total_profiled":1310},"omim":[{"mim_id":"610785","title":"PDLIM1-INTERACTING KINASE 1-LIKE; PDIK1L","url":"https://www.omim.org/entry/610785"},{"mim_id":"605900","title":"PDZ AND LIM DOMAIN PROTEIN 1; PDLIM1","url":"https://www.omim.org/entry/605900"},{"mim_id":"605889","title":"PDZ AND LIM DOMAIN PROTEIN 3; PDLIM3","url":"https://www.omim.org/entry/605889"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Actin filaments","reliability":"Supported"},{"location":"Plasma membrane","reliability":"Additional"},{"location":"Cell Junctions","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal 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Both nonmuscle alpha-actinin-1 and alpha-actinin-4 form complexes with CLP-36, as demonstrated by immunoprecipitation and MALDI-TOF mass spectrometry.\",\n      \"method\": \"Co-immunoprecipitation, MALDI-TOF MS, subcellular localization by fluorescence microscopy, domain deletion analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP with MS confirmation, domain-mapping experiments, replicated across two isoforms and independently confirmed in a second paper (PMID:11110697)\",\n      \"pmids\": [\"10753915\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Human CLP36 (PDLIM1) binds alpha-actinin-1 via its intervening sequence (not the PDZ or LIM domain alone), as shown by yeast two-hybrid analysis mapping to spectrin-like repeats 2 and 3 of alpha-actinin-1. CLP36 associates with actin filaments and stress fibers in activated platelets and endothelial cells and is absent from focal adhesions. The N-terminal PDZ domain plus intervening region, but not the LIM domain alone, targets CLP36 to stress fibers.\",\n      \"method\": \"Co-immunoprecipitation, pull-down assays, yeast two-hybrid, blot overlay, GFP fusion localization in endothelial cells\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (Co-IP, pulldown, Y2H, blot overlay, domain deletion + GFP targeting), single lab with rigorous controls\",\n      \"pmids\": [\"11110697\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"hCLIM1 (PDLIM1) interacts with alpha-actinin-2 (skeletal muscle isoform) via its LIM domain binding to the EF-hand region of alpha-actinin-2, defining a new mode of LIM domain interaction. hCLIM1 colocalizes with alpha-actinin at Z-disks in human myocardium.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence colocalization\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Y2H domain mapping plus Co-IP in a single lab, two orthogonal methods\",\n      \"pmids\": [\"10861853\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"CLP-36 (PDLIM1) acts as an adapter that recruits the novel kinase Clik1 to actin stress fibers via its C-terminal LIM domain. Clik1 is otherwise predominantly nuclear; association with CLP-36 relocalizes it to actin stress fibers, where it disrupts the periodic staining pattern of CLP-36.\",\n      \"method\": \"Yeast two-hybrid, subcellular colocalization, domain deletion analysis\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Y2H interaction mapping plus functional relocalization experiment, single lab\",\n      \"pmids\": [\"11973348\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CLP36 (PDLIM1) is required for actin stress fiber formation and focal adhesion assembly in BeWo cells. RNAi-mediated knockdown caused loss of stress fibers and focal adhesions; rescue required both the PDZ and LIM domains, establishing that both domains are functionally essential.\",\n      \"method\": \"RNAi knockdown, rescue with domain-deletion mutants, fluorescence microscopy\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with defined phenotype plus domain-mutation rescue, single lab\",\n      \"pmids\": [\"17964547\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PDLIM1 (CLP36) is the PDZ domain-containing protein that tethers Plasma Membrane Ca2+-ATPase (PMCA) to the cytoskeleton in resting platelets via PDZ domain interactions with the C-terminal PDZ-binding motif of PMCA4b. CLP36, PMCA, alpha-actinin, and actin co-elute as a ~1,000 kDa complex by gel filtration, and CLP36 colocalizes with PMCA in both resting and activated platelets.\",\n      \"method\": \"Co-immunoprecipitation, LC-MS/MS, GST pull-down, gel filtration chromatography, immunofluorescence microscopy\",\n      \"journal\": \"Thrombosis and haemostasis\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, MS, GST pulldown, gel filtration, colocalization) in single study with rigorous controls\",\n      \"pmids\": [\"17393022\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CLP36 (PDLIM1) interacts with palladin via its PDZ domain binding to the C-terminus of palladin. Palladin silencing suppresses CLP36 localization to stress fibers, and overexpression of the PDZ domain alone inhibits palladin localization to stress fibers. Alpha-actinin, CLP36, and palladin form a protein complex important for actin cytoskeleton regulation.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, siRNA knockdown, overexpression of domain constructs, fluorescence microscopy\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Y2H plus Co-IP plus functional knockdown, single lab\",\n      \"pmids\": [\"19366376\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CLP36 (PDLIM1) forms a complex with alpha-actinin in sensory (DRG) neurons, localizes to actin cytoskeleton in growth cones, and negatively regulates neurite outgrowth: RNAi knockdown of CLP36 induced lamellipodia and increased neurite length and number, whereas overexpression of the PDZ domain alone perturbed neurite outgrowth.\",\n      \"method\": \"RNAi, overexpression of deletion mutants, fluorescence microscopy, co-immunoprecipitation\",\n      \"journal\": \"Journal of neurochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with defined morphological phenotype plus domain overexpression, single lab\",\n      \"pmids\": [\"19780892\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"CLP36 (PDLIM1) interacts with palladin in dorsal root ganglion neurons, forming a complex detectable by co-immunoprecipitation; both proteins colocalize in neurites and cell bodies of primary DRG neurons. Sciatic nerve transection upregulates both CLP36 and palladin mRNAs, with CLP36 being more prominently upregulated, suggesting a specific role in nerve regeneration.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence, qRT-PCR after nerve injury\",\n      \"journal\": \"Neuroscience letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Y2H plus Co-IP in primary neurons, single lab\",\n      \"pmids\": [\"20381583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Alpha-actinin-4 and CLP36 (PDLIM1) form a complex in normal podocytes. siRNA depletion of alpha-actinin-4 markedly reduces CLP36 protein levels. FSGS-associated alpha-actinin-4 mutations (R310Q, Q348R) inhibit complex formation between alpha-actinin-4 and CLP36. Disruption of the alpha-actinin-4–CLP36 complex or reduction of CLP36 significantly inhibits RhoA activity and traction force generation in podocytes.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, mutant overexpression, RhoA activity assay, traction force microscopy\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, siRNA, disease-mutant functional analysis, RhoA assay, traction force), single lab with rigorous controls\",\n      \"pmids\": [\"21680739\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"PDLIM1 exists as part of a complex with FHL1, ACTN1, GSN (gelsolin), and ACTN4, identified by tandem affinity purification from HEK-293 cells and verified by co-immunoprecipitation from mouse heart ventricles and 3D fluorescence microscopy in adult cardiomyocytes.\",\n      \"method\": \"Tandem affinity purification, LC-MS, co-immunoprecipitation, 3D fluorescence microscopy\",\n      \"journal\": \"Molecular bioSystems\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — TAP-MS plus reciprocal Co-IP verification in native tissue, single lab\",\n      \"pmids\": [\"21246116\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The LIM domain of PDLIM1 binds two zinc ions with femtomolar affinity (Kd avg ~2.5×10⁻¹⁴ M), and protein-protein interactions with the C-terminal extension further elevate Zn2+ affinity. Domain stability depends not only on zinc coordination but significantly on protein-protein interactions involving the C-terminus.\",\n      \"method\": \"Thermal denaturation, mass spectrometry, limited proteolysis, circular dichroism, zinc affinity measurements\",\n      \"journal\": \"Journal of inorganic biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple biophysical and biochemical methods characterizing intrinsic biochemical properties in vitro, single lab but comprehensive\",\n      \"pmids\": [\"22922308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CLP36 (PDLIM1) acts as a major inhibitor of GPVI/ITAM signaling in platelets. Mice expressing truncated CLP36 lacking the LIM domain or CLP36 knockout mice displayed hyperactivation (hyperphosphorylation, enhanced Ca2+ mobilization, granule secretion, integrin activation) specifically downstream of GPVI, leading to accelerated thrombus formation in vivo.\",\n      \"method\": \"Genetic knockout and truncation mouse models, platelet functional assays (Ca2+ mobilization, integrin activation, granule secretion), in vivo thrombosis models, phosphoprotein analysis\",\n      \"journal\": \"Circulation research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO plus domain-truncation mouse models with multiple functional readouts and in vivo validation, rigorous controls\",\n      \"pmids\": [\"22955732\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CLP36 and RIL (another ALP/Enigma family member) form a complex with alpha-actinin-1 and palladin on stress fibers. CLP36 depletion in F2408 fibroblasts caused non-oriented stress fiber organization; RIL compensated for this role. CLP36 and RIL have redundant roles in stress fiber formation but distinct effects on stress fiber dynamics.\",\n      \"method\": \"RNAi knockdown, time-lapse microscopy, co-immunoprecipitation, fluorescence microscopy\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with defined phenotype plus Co-IP complex verification, single lab\",\n      \"pmids\": [\"22659164\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CLP36 (PDLIM1) promotes breast cancer cell migration and invasion through interaction with alpha-actinin-1 and alpha-actinin-4. Mutations abolishing alpha-actinin-binding activity eliminated the ability of CLP36 to promote migration. CLP36 depletion or disruption of the CLP36–alpha-actinin complex substantially inhibited Cdc42 activation, cell polarization, and directional migration.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, binding-interface mutagenesis, Cdc42 GTPase activity assay, migration/invasion assays, in vivo metastasis model\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, mutagenesis of binding interface, Cdc42 activity assay, in vivo validation; multiple orthogonal methods in single study\",\n      \"pmids\": [\"24662836\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PDLIM1 interacts with and stabilizes the E-cadherin/β-catenin complex at cell-cell junctions, thereby inhibiting β-catenin nuclear translocation and transcriptional activity and suppressing EMT in colorectal cancer cells. PDLIM1 knockdown increased nuclear β-catenin activity and promoted invasion, while overexpression attenuated EMT.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, overexpression, β-catenin reporter assay, in vivo orthotopic and lung metastasis mouse models\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP interaction, reporter assay for β-catenin activity, KD/OE with defined EMT phenotype, in vivo validation; multiple orthogonal methods\",\n      \"pmids\": [\"26701804\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PDLIM1 inhibits NF-κB-mediated inflammatory signaling by sequestering the p65 subunit of NF-κB in the cytoplasm in an IκBα-independent but alpha-actinin-4-dependent manner. PDLIM1 deficiency leads to increased nuclear p65 levels and enhanced proinflammatory cytokine production in response to innate stimuli.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, subcellular fractionation, nuclear p65 quantification, cytokine ELISA\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, subcellular fractionation, KD with cytokine readout; single lab, multiple methods\",\n      \"pmids\": [\"26679095\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PDLIM1 interacts with the neurotrophin receptor p75NTR (CD271) via its PDZ domain binding to the C-terminal SPV PDZ-binding motif of p75NTR. This interaction is regulated by S425 phosphorylation of p75NTR. The interaction also requires that p75NTR not be phosphorylated at S303 by PKA. shRNA knockdown of PDLIM1 completely ablated p75NTR-mediated glioma invasion in vitro and in vivo.\",\n      \"method\": \"Peptide-based interaction screen, co-immunoprecipitation, phosphorylation mutant analysis, shRNA knockdown, in vivo glioma invasion model\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with phosphomutant dissection plus in vivo shRNA validation, single lab\",\n      \"pmids\": [\"26119933\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PDLIM1 must be degraded via the autophagy-lysosome pathway (dependent on ATG7) to allow proper cytoskeletal reorganization during spermatid differentiation. In atg7-null mice, PDLIM1 accumulates, impairing cytoskeleton organization and leading to defects in flagella biogenesis and cytoplasm removal during spermiogenesis.\",\n      \"method\": \"Conditional knockout mouse model (atg7-null), functional screening, western blot, phenotypic analysis of sperm morphology and motility\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with defined phenotypic readout linking PDLIM1 accumulation to cytoskeletal defects, single lab\",\n      \"pmids\": [\"27310465\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PDLIM1 competitively binds alpha-actinin-4 (ACTN4), leading to dissociation of ACTN4 from F-actin and preventing F-actin overgrowth. Loss of PDLIM1 induces excessive F-actin formation, resulting in dephosphorylation of LATS1 and activation of YAP, promoting HCC metastasis via the Hippo pathway. Asn145 (N145) of PDLIM1 is critical for its interaction with ACTN4, and N145A mutation abolishes this regulatory function.\",\n      \"method\": \"Co-immunoprecipitation, site-directed mutagenesis (N145A), F-actin binding assay, LATS1 phosphorylation assay, YAP activity measurement, in vitro invasion and in vivo metastasis models\",\n      \"journal\": \"Hepatology (Baltimore, Md.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — mutagenesis identifying critical residue, Co-IP, F-actin assays, Hippo pathway signaling readout, in vivo validation; multiple orthogonal methods\",\n      \"pmids\": [\"31509262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PDLIM1 localizes to actin-rich structures generated by bacterial pathogens: it accumulates at sites of Listeria entry, in actin clouds surrounding immotile bacteria, and within actin comet/rocket tails. PDLIM1 is maintained in the actin core of membrane protrusions but absent from the membrane invagination internalizing Listeria. PDLIM1 is also a component of EPEC pedestals and its recruitment is dependent on the bacterial effector Tir.\",\n      \"method\": \"Immunofluorescence microscopy, subcellular localization during bacterial infection, Tir-deletion bacterial mutant analysis\",\n      \"journal\": \"Anatomical record (Hoboken, N.J. : 2007)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiments with mechanistic dissection (Tir-dependence), single lab\",\n      \"pmids\": [\"33022122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CLP36 (PDLIM1) promotes p53-deficient sarcoma progression by inhibiting AIP-4 (ITCH E3 ligase)-dependent proteasomal degradation of YAP1, thereby increasing YAP1 protein levels. CLP36 knockout in mice markedly inhibited p53-deficiency-induced tumorigenesis.\",\n      \"method\": \"Co-immunoprecipitation, genetic KO mouse model, ubiquitination assay, western blot, tumor growth assay\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, in vivo KO model; single lab with multiple methods\",\n      \"pmids\": [\"35836803\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PDLIM1 interacts with hexokinase 2 (HK2) in gastric cancer cells, as demonstrated by co-immunoprecipitation. This interaction mediates glycolysis and cell biological behaviors under glucose deprivation through the Wnt/β-catenin signaling pathway.\",\n      \"method\": \"Co-immunoprecipitation, glucose metabolism assays (glycolytic indicators), western blot, siRNA knockdown and overexpression\",\n      \"journal\": \"Cell and tissue research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP in a single lab with limited mechanistic follow-up\",\n      \"pmids\": [\"37930472\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cblb (an E3 ubiquitin ligase) binds to the PDZ and LIM domains of PDLIM1 and ubiquitinates PDLIM1 at K244, targeting it for proteasome-mediated degradation. In microglia, this Cblb-mediated degradation of PDLIM1 releases NF-κB signaling, promoting pyroptosis. Botulinum toxin A suppresses Cblb activity, thereby preventing PDLIM1 degradation and inhibiting NF-κB-mediated pyroptosis.\",\n      \"method\": \"Mass spectrometry, co-immunoprecipitation, ubiquitination assay (K244 site identification), proteasome inhibition, shRNA knockdown, lentiviral/AAV rescue experiments in vivo\",\n      \"journal\": \"The journal of headache and pain\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS identification + Co-IP + site-specific ubiquitination mapping + in vivo rescue, single lab\",\n      \"pmids\": [\"40696327\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PDLIM1 (CLP-36/hCLIM1) is a scaffold/adapter protein that localizes to actin stress fibers in nonmuscle cells by binding alpha-actinin isoforms (ACTN1, ACTN4) via its PDZ domain and intervening sequence; it recruits binding partners (including the Clik1 kinase and palladin) to actin structures via its LIM domain, regulates F-actin dynamics by competing with ACTN4 for actin binding to control Hippo/LATS1/YAP signaling, sequesters NF-κB p65 in the cytoplasm in an alpha-actinin-4-dependent manner to suppress inflammation, stabilizes the E-cadherin/β-catenin junctional complex to inhibit EMT, and is subject to proteasomal degradation through Cblb-mediated K244 ubiquitination as well as autophagy-lysosome-dependent degradation during spermatogenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PDLIM1 (CLP-36/hCLIM1) is a PDZ-LIM scaffold protein that organizes the actin cytoskeleton and couples it to signaling by tethering alpha-actinin and its associated partners onto actin stress fibers [#0, #1]. Its bipartite architecture underlies this adapter role: the N-terminal PDZ domain plus an intervening sequence binds the spectrin-like repeats of nonmuscle alpha-actinin-1 and alpha-actinin-4 and targets the protein to stress fibers (while the LIM domain alone does not), and the C-terminal LIM domain recruits additional clients such as the Clik1 kinase to those actin structures [#0, #1, #3]. Through these interactions PDLIM1 builds higher-order complexes with palladin and other actin regulators and is itself required for stress fiber and focal adhesion assembly [#4, #6, #13]. Beyond structural scaffolding, PDLIM1 controls Rho-family and Hippo signaling at the actin interface: the alpha-actinin-4 complex governs RhoA activity and traction force generation [#9], the alpha-actinin complex drives Cdc42 activation and directional cell migration [#14], and competitive binding of alpha-actinin-4 to limit F-actin overgrowth restrains LATS1 dephosphorylation and YAP activation [#19]. PDLIM1 additionally functions as a cytoplasmic sequestering hub for transcription factors, retaining NF-kB p65 in the cytoplasm in an alpha-actinin-4-dependent manner to suppress inflammation [#16] and stabilizing the E-cadherin/beta-catenin junctional complex to block beta-catenin nuclear activity and EMT [#15]. PDLIM1 abundance is set by regulated degradation, including Cblb-mediated K244 ubiquitination and proteasomal turnover that releases NF-kB-driven pyroptosis [#23] and ATG7-dependent autophagic clearance required for cytoskeletal remodeling during spermiogenesis [#18]. In platelets, PDLIM1 acts as a major negative regulator of GPVI/ITAM signaling, limiting thrombus formation [#12].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established the founding function of PDLIM1 as a stress-fiber adapter, defining how a PDZ-LIM protein is targeted to the actin cytoskeleton through alpha-actinin binding.\",\n      \"evidence\": \"Co-IP with MALDI-TOF MS, yeast two-hybrid domain mapping, and GFP-fusion localization in nonmuscle, endothelial, and platelet cells\",\n      \"pmids\": [\"10753915\", \"11110697\", \"10861853\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish whether actin association is direct or fully alpha-actinin-mediated\", \"Functional consequence of stress-fiber targeting not yet tested\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Showed PDLIM1 is not just a structural anchor but recruits signaling enzymes to actin, redistributing the otherwise nuclear Clik1 kinase to stress fibers via its LIM domain.\",\n      \"evidence\": \"Yeast two-hybrid and colocalization with domain-deletion analysis\",\n      \"pmids\": [\"11973348\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Clik1 substrates on stress fibers unidentified\", \"Functional output of LIM-mediated kinase recruitment untested\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstrated PDLIM1 is functionally required, not merely associated, for actin stress fiber and focal adhesion assembly, and that both PDZ and LIM domains are essential.\",\n      \"evidence\": \"RNAi knockdown with domain-deletion rescue in BeWo cells\",\n      \"pmids\": [\"17964547\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular step in assembly that PDLIM1 controls unresolved\", \"Cell-type generality of the requirement not established here\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Extended the scaffold concept to membrane-cytoskeleton coupling by showing PDLIM1 tethers the PMCA calcium pump to the actin/alpha-actinin network in platelets.\",\n      \"evidence\": \"Co-IP, LC-MS/MS, GST pulldown, gel filtration of a ~1,000 kDa complex, and colocalization\",\n      \"pmids\": [\"17393022\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence for calcium handling not directly measured\", \"Stoichiometry of the megacomplex undefined\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified palladin as a PDZ-domain partner and placed PDLIM1 in an alpha-actinin/palladin complex with mutual dependence for stress-fiber localization, including in neurons where PDLIM1 negatively regulates neurite outgrowth.\",\n      \"evidence\": \"Y2H, Co-IP, siRNA, and domain-overexpression microscopy in fibroblasts and DRG neurons\",\n      \"pmids\": [\"19366376\", \"19780892\", \"20381583\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signaling pathway linking the complex to outgrowth suppression unknown\", \"Relevance of nerve-injury upregulation to regeneration not functionally tested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Linked the PDLIM1/alpha-actinin-4 complex to active cytoskeletal mechanics and disease, showing it controls RhoA activity and traction force and is disrupted by FSGS-causing alpha-actinin-4 mutations.\",\n      \"evidence\": \"Co-IP, siRNA, disease-mutant analysis, RhoA assay, and traction force microscopy in podocytes; TAP-MS complex definition in cardiac tissue\",\n      \"pmids\": [\"21680739\", \"21246116\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which the complex regulates RhoA not defined\", \"Whether reduced PDLIM1 levels are cause or consequence of complex loss unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined PDLIM1's intrinsic biochemistry (femtomolar dual-zinc LIM domain stabilized by C-terminal interactions) and revealed a genetically validated negative-regulatory role in platelet GPVI/ITAM signaling and thrombosis.\",\n      \"evidence\": \"Biophysical zinc-affinity measurements in vitro; knockout and LIM-truncation mouse models with platelet functional assays and in vivo thrombosis; plus redundancy analysis with RIL on stress fibers\",\n      \"pmids\": [\"22922308\", \"22955732\", \"22659164\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular target of PDLIM1 in the GPVI cascade not identified\", \"Extent of functional redundancy with other ALP/Enigma members in vivo unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Established PDLIM1 as a pro-migratory effector in cancer that drives Cdc42 activation, cell polarization, and metastasis strictly through its alpha-actinin interaction.\",\n      \"evidence\": \"Binding-interface mutagenesis, Cdc42 activity assay, migration/invasion assays, and in vivo metastasis in breast cancer cells\",\n      \"pmids\": [\"24662836\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Link from the actin complex to Cdc42 GEF/GAP regulation undefined\", \"Context-dependence versus tumor-suppressive roles in other cancers unreconciled\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Revealed PDLIM1 as a cytoplasmic sequestering hub controlling transcription-factor localization—stabilizing E-cadherin/beta-catenin junctions to block EMT and retaining NF-kB p65 in the cytoplasm to suppress inflammation.\",\n      \"evidence\": \"Co-IP, knockdown/overexpression, reporter assays, subcellular fractionation, cytokine ELISA, and in vivo metastasis models; plus PDZ-mediated p75NTR binding driving glioma invasion\",\n      \"pmids\": [\"26701804\", \"26679095\", \"26119933\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How a single scaffold reconciles tumor-suppressive (EMT/NF-kB) and tumor-promoting (p75NTR) outputs unresolved\", \"Whether p65 sequestration is direct or alpha-actinin-4-bridged not fully dissected\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed PDLIM1 abundance must be actively lowered for cytoskeletal remodeling, with ATG7-dependent autophagic degradation required during spermatid differentiation.\",\n      \"evidence\": \"atg7-null conditional knockout mice with western blot and sperm morphology/motility phenotyping\",\n      \"pmids\": [\"27310465\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Autophagy receptor selecting PDLIM1 unidentified\", \"Whether PDLIM1 accumulation is sufficient to cause the spermiogenesis defect not isolated\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Provided a mechanistic link from PDLIM1 to Hippo signaling, showing competitive sequestration of alpha-actinin-4 from F-actin (via residue N145) limits F-actin overgrowth, preserving LATS1 phosphorylation and restraining YAP-driven HCC metastasis; also placed PDLIM1 at pathogen-induced actin structures.\",\n      \"evidence\": \"N145A mutagenesis, Co-IP, F-actin binding and LATS1 phosphorylation/YAP assays with in vivo metastasis; immunofluorescence at Listeria/EPEC actin structures with Tir-mutant analysis\",\n      \"pmids\": [\"31509262\", \"33022122\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How F-actin level changes are transduced to the LATS1 kinase cassette not detailed\", \"Functional role of PDLIM1 at bacterial actin structures untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified a second, opposing route by which PDLIM1 controls YAP—protecting YAP1 from ITCH/AIP-4-dependent proteasomal degradation to promote p53-deficient sarcoma.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, and CLP36-knockout mouse tumorigenesis model\",\n      \"pmids\": [\"35836803\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How PDLIM1 shields YAP1 from ITCH mechanistically unclear\", \"Reconciliation with the F-actin/LATS1 route to YAP regulation not addressed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Suggested a metabolic interaction in which PDLIM1 binds hexokinase 2 to influence glycolysis under glucose deprivation via Wnt/beta-catenin signaling.\",\n      \"evidence\": \"Single Co-IP with glycolysis assays and knockdown/overexpression in gastric cancer cells\",\n      \"pmids\": [\"37930472\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP without reciprocal or orthogonal validation\", \"Direct versus indirect HK2 association undetermined\", \"Mechanistic link to Wnt/beta-catenin not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined how PDLIM1 protein levels are set by the ubiquitin-proteasome system, identifying Cblb as the E3 ligase ubiquitinating K244, with degradation releasing NF-kB-driven microglial pyroptosis.\",\n      \"evidence\": \"Mass spectrometry, Co-IP, K244 site-specific ubiquitination mapping, proteasome inhibition, and in vivo shRNA/AAV rescue\",\n      \"pmids\": [\"40696327\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signals controlling Cblb-PDLIM1 engagement unknown\", \"Whether NF-kB release reflects loss of p65 sequestration not directly connected to the 2015 mechanism\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PDLIM1 toggles between tumor-suppressive (E-cadherin/beta-catenin stabilization, NF-kB sequestration, F-actin/LATS1-mediated YAP restraint) and tumor-promoting (Cdc42 migration, YAP1 stabilization, p75NTR invasion) outputs remains the central unresolved question.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model reconciling opposing context-dependent roles\", \"Structural basis distinguishing competing partner-selection states unknown\", \"Upstream signals dictating which complex PDLIM1 forms not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 3, 6, 5]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 1, 4, 13, 19]},\n      {\"term_id\": \"GO:0140313\", \"supporting_discovery_ids\": [15, 16]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9, 14, 19, 12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 1, 4, 13, 7]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [15, 16]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [19, 9, 14, 16]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [9, 15, 19, 21]},\n      {\"term_id\": \"R-HSA-109582\", \"supporting_discovery_ids\": [5, 12]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [16, 23]}\n    ],\n    \"complexes\": [\n      \"PDLIM1/alpha-actinin/palladin actin stress-fiber complex\",\n      \"PDLIM1/PMCA4b/alpha-actinin/actin platelet complex\",\n      \"E-cadherin/beta-catenin junctional complex\"\n    ],\n    \"partners\": [\n      \"ACTN1\",\n      \"ACTN4\",\n      \"ACTN2\",\n      \"PALLD\",\n      \"Clik1\",\n      \"p65/RELA\",\n      \"YAP1\",\n      \"CBLB\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}