{"gene":"ILKAP","run_date":"2026-06-10T01:55:23","timeline":{"discoveries":[{"year":2001,"finding":"ILKAP, a PP2C family serine/threonine phosphatase, was identified as a binding partner of integrin-linked kinase ILK1 via yeast two-hybrid screen; their association is independent of the catalytic activity of either partner as confirmed by co-precipitation and two-hybrid assays.","method":"Yeast two-hybrid screen, co-precipitation","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal yeast two-hybrid and co-precipitation, replicated in follow-up studies","pmids":["11331582"],"is_preprint":false},{"year":2001,"finding":"Conditional expression of ILKAP in HEK 293 cells selectively inhibited ECM- and growth factor-stimulated ILK1 kinase activity but did not inhibit Raf-1 kinase activity, demonstrating specificity for ILK1 signaling.","method":"Conditional expression, immune complex kinase assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — catalytic mutant H154D used as control, replicated in follow-up work","pmids":["11331582"],"is_preprint":false},{"year":2001,"finding":"Catalytically active ILKAP selectively inhibited IGF-1-stimulated GSK3β phosphorylation on Ser9 but did not affect PKB/AKT phosphorylation on Ser473, establishing differential downstream selectivity; catalytic mutant H154D failed to show this inhibition.","method":"Conditional expression, phosphorylation assay with catalytic mutant control (H154D)","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — active-site mutagenesis used, replicated by siRNA experiments in follow-up","pmids":["11331582","14990992"],"is_preprint":false},{"year":2001,"finding":"Active ILKAP (but not H154D mutant or the related PP2Cα) selectively inhibited transactivation of a Tcf/Lef reporter gene (TOPFlash) in 293 cells, placing ILKAP upstream of Wnt/GSK3β pathway components.","method":"Reporter gene assay (TOPFlash luciferase), active-site mutagenesis","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — active-site mutant and paralog controls used in single lab study","pmids":["11331582"],"is_preprint":false},{"year":2004,"finding":"siRNA silencing of endogenous ILKAP stimulated GSK3β phosphorylation at S9 with no effect on PKB S473 phosphorylation, confirming endogenous ILKAP selectively targets the ILK–GSK3β axis.","method":"siRNA knockdown, phosphorylation assay","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Strong — siRNA loss-of-function confirms gain-of-function data, two orthogonal methods","pmids":["14990992"],"is_preprint":false},{"year":2004,"finding":"ILKAP inhibition of ILK selectively reduced cyclin D1 expression (an ILK–GSK3β signaling target), increased proportion of LNCaP cells in G1, and inhibited anchorage-independent growth; rescue by ILK overexpression but not dominant-negative ILK confirmed pathway specificity.","method":"Stable/transient expression, siRNA, immune complex kinase assay, cell cycle analysis, soft agar assay, ILK rescue experiment","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal functional readouts with epistasis rescue experiment in single lab","pmids":["14990992"],"is_preprint":false},{"year":2008,"finding":"ILKAP enhances CRM1-dependent nuclear export of ILK, thereby controlling ILK nucleo-cytoplasmic shuttling; nuclear ILK promotes DNA synthesis in epidermal keratinocytes and this is sensitive to inhibition by ILKAP.","method":"Live cell imaging, nuclear fractionation, CRM1 inhibitor (leptomycin B), DNA synthesis assay","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional consequence (DNA synthesis), single lab","pmids":["18635968"],"is_preprint":false},{"year":2012,"finding":"ILKAP binds phosphopeptides corresponding to substrates of PP2Cδ including p38, ATM, Chk1, Chk2, and RSK2; binding requires phosphorylation on Ser or Thr and is influenced by flanking sequence context, establishing substrate-binding affinity profile.","method":"Solid-phase phosphopeptide affinity pull-down from cell lysates","journal":"Molecular bioSystems","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical pull-down with multiple phosphopeptide substrates, single lab","pmids":["22348942"],"is_preprint":false},{"year":2013,"finding":"ILKAP is predominantly a nuclear protein; its nuclear import is mediated by a nuclear localization signal (NLS) in the N-terminal region (amino acids 71–86), with Lys-78 and Arg-79 critical for binding to importin α1, α3, and α5; NLS-deleted ILKAP redistributes to cytoplasm.","method":"Immunofluorescence, subcellular fractionation, co-immunoprecipitation with importins, NLS deletion and point mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — mutagenesis with multiple orthogonal methods (imaging, fractionation, co-IP) in single lab","pmids":["23329845"],"is_preprint":false},{"year":2013,"finding":"Nuclear ILKAP interacts with RSK2 and induces apoptosis by inhibiting RSK2 activity and down-regulating cyclin D1 expression (a downstream RSK2 substrate).","method":"Co-immunoprecipitation, RSK2 kinase activity assay, Western blot for cyclin D1, apoptosis assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus functional kinase assay, single lab, consistent with phosphopeptide binding data","pmids":["23329845"],"is_preprint":false},{"year":2015,"finding":"ILKAP knockdown in p53-wildtype GBM cells reduces radiation-induced DNA-PK phosphorylation, establishing ILKAP as required for DNA-PK activation and thereby contributing to radioresistance in a p53-dependent manner.","method":"siRNA knockdown, γH2AX/53BP1 foci assay, phospho-DNAPK Western blot, clonogenic survival assay","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockdown with defined molecular readout (phospho-DNAPK), single lab","pmids":["26460618"],"is_preprint":false},{"year":2016,"finding":"In ovarian cancer cells, ILKAP dephosphorylates p90RSK (RSK1/RSK2) and AKT/ILK; ILKAP silencing protects cells from cisplatin-induced death by simultaneously activating RSK, ILK, and AKT, establishing ILKAP as a regulatory hub requiring combined RSK and ILK inhibition to reverse its loss.","method":"siRNA knockdown, Western blot (phosphorylation), cell viability/apoptosis assay, pharmacological kinase inhibition","journal":"European journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with multiple kinase readouts, single lab, multiple orthogonal methods","pmids":["27065457"],"is_preprint":false},{"year":2017,"finding":"MAEL promotes lysosome-dependent degradation of ILKAP protein, leading to increased phosphorylation of ILKAP substrates p38, CHK1, and RSK2; ILKAP overexpression reverses the oncogenic effects of MAEL in vitro and in vivo.","method":"Co-expression/silencing, Western blot, lysosome inhibitor experiments, xenograft model, adenoviral ILKAP overexpression rescue","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — lysosomal degradation mechanism with rescue experiment, single lab","pmids":["29371914"],"is_preprint":false},{"year":2018,"finding":"ILKAP physically interacts with HIF-1α and dephosphorylates it; this interaction promotes HIF-1α–p53 interaction and apoptosis under severe hypoxia.","method":"Co-immunoprecipitation, luciferase reporter assay (hypoxia-response element), overexpression/shRNA loss-of-function, trypan blue viability assay","journal":"Cellular physiology and biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus functional reporter and viability assays, single lab","pmids":["29742494"],"is_preprint":false},{"year":2024,"finding":"ILKAP interacts with β-catenin, dephosphorylates GSK3β and CK1 (reducing β-catenin ubiquitination and degradation), and mediates binding between TCF4 and β-catenin to enhance Wnt target gene expression; localizes to both nucleus and cytoplasm in HCC cells.","method":"Co-immunoprecipitation, Western blot (phosphorylation, ubiquitination), immunofluorescence localization, luciferase reporter, in vitro and zebrafish xenograft in vivo metastasis assays","journal":"Advanced biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical readouts and in vivo model, single lab","pmids":["38379270"],"is_preprint":false},{"year":2025,"finding":"ILKAP knockdown reduces PGAM1 expression and suppresses glycolysis (measured by extracellular acidification rate); restoring PGAM1 in ILKAP-knockdown cells rescues proliferation and invasion, placing PGAM1 downstream of ILKAP in metabolic reprogramming.","method":"siRNA knockdown, RNA sequencing, PGAM1 rescue overexpression, extracellular acidification rate measurement, xenograft model","journal":"Frontiers of medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis rescue experiment with transcriptomic and metabolic readouts, single lab","pmids":["41454076"],"is_preprint":false}],"current_model":"ILKAP is a PP2C-family serine/threonine phosphatase that localizes predominantly to the nucleus (via an importin-dependent NLS) and also to the cytoplasm; it directly binds and inhibits ILK1 in a catalysis-dependent manner, selectively suppressing GSK3β (but not AKT) phosphorylation to dampen Wnt/Tcf signaling and cyclin D1 expression, while in the nucleus it dephosphorylates and inactivates RSK2, HIF-1α, and (in some contexts) stabilizes β-catenin by dephosphorylating its regulators GSK3β and CK1; its protein level is regulated by MAEL-driven lysosomal degradation, and loss of ILKAP activates pro-survival kinases (ILK, AKT, RSK, DNA-PK) to confer resistance to genotoxic stresses."},"narrative":{"mechanistic_narrative":"ILKAP is a PP2C-family serine/threonine phosphatase that functions as a negative regulator of integrin-linked kinase (ILK) signaling and a broader hub controlling pro-survival kinase pathways and Wnt-driven gene expression [PMID:11331582, PMID:14990992]. It was first identified as a catalysis-independent binding partner of ILK1 that, when catalytically active, selectively inhibits ECM- and growth-factor-stimulated ILK kinase activity without affecting Raf-1 [PMID:11331582]. Downstream, active ILKAP selectively blocks ILK-dependent GSK3β Ser9 phosphorylation while sparing AKT Ser473, and endogenous loss-of-function by siRNA mirrors this selectivity, defining the ILK–GSK3β axis as its principal target [PMID:11331582, PMID:14990992]. Through this axis ILKAP suppresses Tcf/Lef-dependent transcription and cyclin D1 expression, arresting cells in G1 and limiting anchorage-independent growth [PMID:11331582, PMID:14990992]. ILKAP is predominantly nuclear, imported via an N-terminal NLS (residues 71–86, with Lys-78/Arg-79 critical) that binds importin α1/α3/α5 [PMID:23329845], and it also controls CRM1-dependent nuclear export of ILK [PMID:18635968]. In the nucleus it binds and dephosphorylates additional substrates including RSK2 and HIF-1α to promote apoptosis [PMID:23329845, PMID:29742494], and it binds phosphopeptide substrates of PP2Cδ such as p38, ATM, Chk1, Chk2, and RSK2 [PMID:22348942]. ILKAP loss broadly activates pro-survival kinases (ILK, AKT, RSK, DNA-PK), conferring resistance to genotoxic and chemotherapeutic stress [PMID:26460618, PMID:27065457], and its protein level is lowered by MAEL-driven lysosomal degradation [PMID:29371914]. In hepatocellular carcinoma ILKAP can instead stabilize β-catenin by dephosphorylating GSK3β and CK1 and bridging TCF4–β-catenin to enhance Wnt targets [PMID:38379270], and it supports glycolytic reprogramming via PGAM1 [PMID:41454076].","teleology":[{"year":2001,"claim":"Established that ILKAP physically associates with ILK1 and acts as a phosphatase that selectively suppresses ILK signaling, defining its core function as a negative regulator of ILK rather than a general phosphatase.","evidence":"Yeast two-hybrid, co-precipitation, and conditional expression with immune-complex kinase assays plus an H154D catalytic-dead control in HEK293 cells","pmids":["11331582"],"confidence":"High","gaps":["Direct dephosphorylation of ILK or an intermediate not biochemically resolved","Binding shown to be catalysis-independent but functional inhibition catalysis-dependent — coupling mechanism unexplained"]},{"year":2001,"claim":"Defined downstream selectivity by showing ILKAP blocks ILK→GSK3β Ser9 phosphorylation and Tcf/Lef transactivation but spares AKT, placing it specifically on the Wnt/GSK3β branch.","evidence":"Conditional expression with phosphorylation assays, TOPFlash reporter, and active-site/paralog (PP2Cα) controls","pmids":["11331582"],"confidence":"High","gaps":["Whether GSK3β is a direct ILKAP substrate or an indirect consequence of ILK inhibition not distinguished"]},{"year":2004,"claim":"Confirmed via endogenous loss-of-function that ILKAP physiologically targets the ILK–GSK3β axis and links its activity to cell-cycle and growth control.","evidence":"siRNA knockdown with phosphorylation assays, cyclin D1 readout, cell-cycle and soft-agar assays, and ILK rescue in LNCaP cells","pmids":["14990992"],"confidence":"High","gaps":["Cyclin D1 regulation inferred through ILK–GSK3β; alternative inputs not excluded"]},{"year":2008,"claim":"Extended ILKAP function to spatial control of ILK by showing it promotes CRM1-dependent nuclear export of ILK, coupling its regulation to DNA synthesis.","evidence":"Live-cell imaging, nuclear fractionation, leptomycin B treatment, and DNA synthesis assays in keratinocytes","pmids":["18635968"],"confidence":"Medium","gaps":["Mechanism by which ILKAP enhances CRM1 export unresolved","Single cell-type context"]},{"year":2012,"claim":"Characterized ILKAP substrate-binding preferences, showing phospho-dependent recognition of PP2Cδ substrates and implicating it in DNA-damage and stress kinase signaling.","evidence":"Solid-phase phosphopeptide affinity pull-downs (p38, ATM, Chk1, Chk2, RSK2) from cell lysates","pmids":["22348942"],"confidence":"Medium","gaps":["Binding affinity does not establish catalytic dephosphorylation of these substrates in cells","Flanking-context determinants only partially mapped"]},{"year":2013,"claim":"Localized ILKAP to the nucleus via a defined importin-binding NLS and identified nuclear RSK2 as a substrate whose inhibition drives apoptosis.","evidence":"NLS deletion/point mutagenesis, immunofluorescence, fractionation, importin co-IP, plus RSK2 kinase and apoptosis assays","pmids":["23329845"],"confidence":"High","gaps":["Whether nuclear vs cytoplasmic pools have distinct substrate repertoires not dissected","RSK2 dephosphorylation site not mapped"]},{"year":2015,"claim":"Implicated ILKAP in DNA-damage survival signaling by showing it is required for radiation-induced DNA-PK activation in a p53-dependent manner.","evidence":"siRNA knockdown with γH2AX/53BP1 foci, phospho-DNA-PK blots, and clonogenic survival in GBM cells","pmids":["26460618"],"confidence":"Medium","gaps":["Direct vs indirect effect on DNA-PK phosphorylation unresolved","p53-dependence mechanism not defined"]},{"year":2016,"claim":"Positioned ILKAP as a multi-kinase regulatory hub whose loss confers chemoresistance by simultaneously activating RSK, ILK, and AKT.","evidence":"siRNA knockdown, phospho-Western blots, viability/apoptosis assays, and combined pharmacological kinase inhibition in ovarian cancer cells","pmids":["27065457"],"confidence":"Medium","gaps":["Which kinase dephosphorylations are direct not established","Single tumor context"]},{"year":2017,"claim":"Identified MAEL-driven lysosomal degradation as a mechanism controlling ILKAP protein level and its substrate phosphorylation in tumors.","evidence":"Co-expression/silencing, lysosome inhibitors, substrate phospho-blots, xenografts, and adenoviral ILKAP rescue","pmids":["29371914"],"confidence":"Medium","gaps":["Molecular route of lysosomal targeting (e.g. direct MAEL interaction) not defined"]},{"year":2018,"claim":"Added HIF-1α as a nuclear ILKAP substrate, linking ILKAP to hypoxic apoptosis via HIF-1α–p53 interaction.","evidence":"Co-IP, HRE luciferase reporter, overexpression/shRNA, and viability assays under hypoxia","pmids":["29742494"],"confidence":"Medium","gaps":["HIF-1α dephosphorylation site not identified","Single-lab functional model"]},{"year":2024,"claim":"Revealed a context-dependent pro-Wnt role in hepatocellular carcinoma where ILKAP stabilizes β-catenin and bridges TCF4–β-catenin, contrasting with its earlier Wnt-suppressive activity.","evidence":"Co-IP, phospho/ubiquitination blots, immunofluorescence, luciferase reporter, and zebrafish xenograft metastasis assays","pmids":["38379270"],"confidence":"Medium","gaps":["Reconciliation with the earlier GSK3β/Tcf-suppressive model not addressed","Direct dephosphorylation of CK1 vs GSK3β priority unresolved"]},{"year":2025,"claim":"Connected ILKAP to metabolic reprogramming by placing PGAM1-dependent glycolysis downstream of ILKAP for proliferation and invasion.","evidence":"siRNA knockdown, RNA-seq, ECAR measurement, and PGAM1 rescue in xenografts","pmids":["41454076"],"confidence":"Medium","gaps":["Mechanism linking ILKAP phosphatase activity to PGAM1 expression unknown","Direct vs transcriptional control unclear"]},{"year":null,"claim":"How ILKAP's context determines whether it suppresses or promotes Wnt/β-catenin signaling, and the structural basis coupling its catalysis-independent ILK binding to catalysis-dependent inhibition, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the ILKAP–ILK complex","Direct catalytic substrates vs indirect effects not systematically separated","Determinants of opposite Wnt outcomes across tumor types unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,9,13,14]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[2,4,9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,11]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[8,9,14]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[8,14]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,2,3,4]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[5,9]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[10]}],"complexes":[],"partners":["ILK","RSK2","HIF1A","CTNNB1","TCF4","KPNA2","MAEL"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H0C8","full_name":"Integrin-linked kinase-associated serine/threonine phosphatase 2C","aliases":[],"length_aa":392,"mass_kda":42.9,"function":"Protein phosphatase that may play a role in regulation of cell cycle progression via dephosphorylation of its substrates whose appropriate phosphorylation states might be crucial for cell proliferation. Selectively associates with integrin linked kinase (ILK), to modulate cell adhesion and growth factor signaling. Inhibits the ILK-GSK3B signaling axis and may play an important role in inhibiting oncogenic transformation","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9H0C8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ILKAP","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ILKAP","total_profiled":1310},"omim":[{"mim_id":"618909","title":"ILK-ASSOCIATED SERINE/THREONINE PHOSPHATASE; ILKAP","url":"https://www.omim.org/entry/618909"},{"mim_id":"603348","title":"HYPOXIA-INDUCIBLE FACTOR 1, ALPHA SUBUNIT; HIF1A","url":"https://www.omim.org/entry/603348"},{"mim_id":"602366","title":"INTEGRIN-LINKED KINASE; ILK","url":"https://www.omim.org/entry/602366"},{"mim_id":"300075","title":"RIBOSOMAL PROTEIN S6 KINASE A3; RPS6KA3","url":"https://www.omim.org/entry/300075"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ILKAP"},"hgnc":{"alias_symbol":["DKFZP434J2031","FLJ10181","PPM1O"],"prev_symbol":[]},"alphafold":{"accession":"Q9H0C8","domains":[{"cath_id":"3.60.40.10","chopping":"105-390","consensus_level":"medium","plddt":95.8969,"start":105,"end":390}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H0C8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H0C8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H0C8-F1-predicted_aligned_error_v6.png","plddt_mean":81.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ILKAP","jax_strain_url":"https://www.jax.org/strain/search?query=ILKAP"},"sequence":{"accession":"Q9H0C8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H0C8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H0C8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H0C8"}},"corpus_meta":[{"pmid":"11331582","id":"PMC_11331582","title":"Modulation of integrin signal transduction by ILKAP, a protein phosphatase 2C associating with the integrin-linked kinase, ILK1.","date":"2001","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/11331582","citation_count":120,"is_preprint":false},{"pmid":"14990992","id":"PMC_14990992","title":"ILKAP regulates ILK signaling and inhibits anchorage-independent growth.","date":"2004","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/14990992","citation_count":69,"is_preprint":false},{"pmid":"18635968","id":"PMC_18635968","title":"Modulation of integrin-linked kinase nucleo-cytoplasmic shuttling by ILKAP and CRM1.","date":"2008","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/18635968","citation_count":22,"is_preprint":false},{"pmid":"29371914","id":"PMC_29371914","title":"MAEL contributes to gastric cancer progression by promoting ILKAP degradation.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29371914","citation_count":20,"is_preprint":false},{"pmid":"26460618","id":"PMC_26460618","title":"ILKAP, ILK and PINCH1 control cell survival of p53-wildtype glioblastoma cells after irradiation.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26460618","citation_count":13,"is_preprint":false},{"pmid":"24743186","id":"PMC_24743186","title":"Involvement of ANXA5 and ILKAP in susceptibility to malignant melanoma.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24743186","citation_count":13,"is_preprint":false},{"pmid":"23329845","id":"PMC_23329845","title":"Characterization of nuclear localization signal in the N terminus of integrin-linked kinase-associated phosphatase (ILKAP) and its essential role in the down-regulation of RSK2 protein signaling.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23329845","citation_count":10,"is_preprint":false},{"pmid":"27065457","id":"PMC_27065457","title":"The integrin-linked kinase-associated phosphatase (ILKAP) is a regulatory hub of ovarian cancer cell susceptibility to platinum drugs.","date":"2016","source":"European journal of cancer (Oxford, England : 1990)","url":"https://pubmed.ncbi.nlm.nih.gov/27065457","citation_count":9,"is_preprint":false},{"pmid":"22348942","id":"PMC_22348942","title":"Probing protein phosphatase substrate binding: affinity pull-down of ILKAP phosphatase 2C with phosphopeptides.","date":"2012","source":"Molecular bioSystems","url":"https://pubmed.ncbi.nlm.nih.gov/22348942","citation_count":6,"is_preprint":false},{"pmid":"29742494","id":"PMC_29742494","title":"ILKAP Binding to and Dephosphorylating HIF-1α is Essential for Apoptosis Induced by Severe Hypoxia.","date":"2018","source":"Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/29742494","citation_count":4,"is_preprint":false},{"pmid":"25872452","id":"PMC_25872452","title":"Endometrial ILKAP expression among patients with endometriosis and its association with clinical characteristics.","date":"2015","source":"International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics","url":"https://pubmed.ncbi.nlm.nih.gov/25872452","citation_count":2,"is_preprint":false},{"pmid":"38379270","id":"PMC_38379270","title":"ILKAP Promotes the Metastasis of Hepatocellular Carcinoma Cells by Inhibiting β-Catenin Degradation and Enhancing the WNT Signaling Pathway.","date":"2024","source":"Advanced biology","url":"https://pubmed.ncbi.nlm.nih.gov/38379270","citation_count":2,"is_preprint":false},{"pmid":"41454076","id":"PMC_41454076","title":"ILKAP drives hepatocellular carcinoma progression by modulating PGAM1-mediated glycolytic reprogramming.","date":"2025","source":"Frontiers of medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41454076","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8669,"output_tokens":3469,"usd":0.039021,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11139,"output_tokens":4216,"usd":0.080547,"stage2_stop_reason":"end_turn"},"total_usd":0.119568,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"ILKAP, a PP2C family serine/threonine phosphatase, was identified as a binding partner of integrin-linked kinase ILK1 via yeast two-hybrid screen; their association is independent of the catalytic activity of either partner as confirmed by co-precipitation and two-hybrid assays.\",\n      \"method\": \"Yeast two-hybrid screen, co-precipitation\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal yeast two-hybrid and co-precipitation, replicated in follow-up studies\",\n      \"pmids\": [\"11331582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Conditional expression of ILKAP in HEK 293 cells selectively inhibited ECM- and growth factor-stimulated ILK1 kinase activity but did not inhibit Raf-1 kinase activity, demonstrating specificity for ILK1 signaling.\",\n      \"method\": \"Conditional expression, immune complex kinase assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — catalytic mutant H154D used as control, replicated in follow-up work\",\n      \"pmids\": [\"11331582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Catalytically active ILKAP selectively inhibited IGF-1-stimulated GSK3β phosphorylation on Ser9 but did not affect PKB/AKT phosphorylation on Ser473, establishing differential downstream selectivity; catalytic mutant H154D failed to show this inhibition.\",\n      \"method\": \"Conditional expression, phosphorylation assay with catalytic mutant control (H154D)\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — active-site mutagenesis used, replicated by siRNA experiments in follow-up\",\n      \"pmids\": [\"11331582\", \"14990992\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Active ILKAP (but not H154D mutant or the related PP2Cα) selectively inhibited transactivation of a Tcf/Lef reporter gene (TOPFlash) in 293 cells, placing ILKAP upstream of Wnt/GSK3β pathway components.\",\n      \"method\": \"Reporter gene assay (TOPFlash luciferase), active-site mutagenesis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — active-site mutant and paralog controls used in single lab study\",\n      \"pmids\": [\"11331582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"siRNA silencing of endogenous ILKAP stimulated GSK3β phosphorylation at S9 with no effect on PKB S473 phosphorylation, confirming endogenous ILKAP selectively targets the ILK–GSK3β axis.\",\n      \"method\": \"siRNA knockdown, phosphorylation assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — siRNA loss-of-function confirms gain-of-function data, two orthogonal methods\",\n      \"pmids\": [\"14990992\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"ILKAP inhibition of ILK selectively reduced cyclin D1 expression (an ILK–GSK3β signaling target), increased proportion of LNCaP cells in G1, and inhibited anchorage-independent growth; rescue by ILK overexpression but not dominant-negative ILK confirmed pathway specificity.\",\n      \"method\": \"Stable/transient expression, siRNA, immune complex kinase assay, cell cycle analysis, soft agar assay, ILK rescue experiment\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal functional readouts with epistasis rescue experiment in single lab\",\n      \"pmids\": [\"14990992\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"ILKAP enhances CRM1-dependent nuclear export of ILK, thereby controlling ILK nucleo-cytoplasmic shuttling; nuclear ILK promotes DNA synthesis in epidermal keratinocytes and this is sensitive to inhibition by ILKAP.\",\n      \"method\": \"Live cell imaging, nuclear fractionation, CRM1 inhibitor (leptomycin B), DNA synthesis assay\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional consequence (DNA synthesis), single lab\",\n      \"pmids\": [\"18635968\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"ILKAP binds phosphopeptides corresponding to substrates of PP2Cδ including p38, ATM, Chk1, Chk2, and RSK2; binding requires phosphorylation on Ser or Thr and is influenced by flanking sequence context, establishing substrate-binding affinity profile.\",\n      \"method\": \"Solid-phase phosphopeptide affinity pull-down from cell lysates\",\n      \"journal\": \"Molecular bioSystems\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical pull-down with multiple phosphopeptide substrates, single lab\",\n      \"pmids\": [\"22348942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"ILKAP is predominantly a nuclear protein; its nuclear import is mediated by a nuclear localization signal (NLS) in the N-terminal region (amino acids 71–86), with Lys-78 and Arg-79 critical for binding to importin α1, α3, and α5; NLS-deleted ILKAP redistributes to cytoplasm.\",\n      \"method\": \"Immunofluorescence, subcellular fractionation, co-immunoprecipitation with importins, NLS deletion and point mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — mutagenesis with multiple orthogonal methods (imaging, fractionation, co-IP) in single lab\",\n      \"pmids\": [\"23329845\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Nuclear ILKAP interacts with RSK2 and induces apoptosis by inhibiting RSK2 activity and down-regulating cyclin D1 expression (a downstream RSK2 substrate).\",\n      \"method\": \"Co-immunoprecipitation, RSK2 kinase activity assay, Western blot for cyclin D1, apoptosis assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus functional kinase assay, single lab, consistent with phosphopeptide binding data\",\n      \"pmids\": [\"23329845\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ILKAP knockdown in p53-wildtype GBM cells reduces radiation-induced DNA-PK phosphorylation, establishing ILKAP as required for DNA-PK activation and thereby contributing to radioresistance in a p53-dependent manner.\",\n      \"method\": \"siRNA knockdown, γH2AX/53BP1 foci assay, phospho-DNAPK Western blot, clonogenic survival assay\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockdown with defined molecular readout (phospho-DNAPK), single lab\",\n      \"pmids\": [\"26460618\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In ovarian cancer cells, ILKAP dephosphorylates p90RSK (RSK1/RSK2) and AKT/ILK; ILKAP silencing protects cells from cisplatin-induced death by simultaneously activating RSK, ILK, and AKT, establishing ILKAP as a regulatory hub requiring combined RSK and ILK inhibition to reverse its loss.\",\n      \"method\": \"siRNA knockdown, Western blot (phosphorylation), cell viability/apoptosis assay, pharmacological kinase inhibition\",\n      \"journal\": \"European journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with multiple kinase readouts, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"27065457\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"MAEL promotes lysosome-dependent degradation of ILKAP protein, leading to increased phosphorylation of ILKAP substrates p38, CHK1, and RSK2; ILKAP overexpression reverses the oncogenic effects of MAEL in vitro and in vivo.\",\n      \"method\": \"Co-expression/silencing, Western blot, lysosome inhibitor experiments, xenograft model, adenoviral ILKAP overexpression rescue\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — lysosomal degradation mechanism with rescue experiment, single lab\",\n      \"pmids\": [\"29371914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ILKAP physically interacts with HIF-1α and dephosphorylates it; this interaction promotes HIF-1α–p53 interaction and apoptosis under severe hypoxia.\",\n      \"method\": \"Co-immunoprecipitation, luciferase reporter assay (hypoxia-response element), overexpression/shRNA loss-of-function, trypan blue viability assay\",\n      \"journal\": \"Cellular physiology and biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus functional reporter and viability assays, single lab\",\n      \"pmids\": [\"29742494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ILKAP interacts with β-catenin, dephosphorylates GSK3β and CK1 (reducing β-catenin ubiquitination and degradation), and mediates binding between TCF4 and β-catenin to enhance Wnt target gene expression; localizes to both nucleus and cytoplasm in HCC cells.\",\n      \"method\": \"Co-immunoprecipitation, Western blot (phosphorylation, ubiquitination), immunofluorescence localization, luciferase reporter, in vitro and zebrafish xenograft in vivo metastasis assays\",\n      \"journal\": \"Advanced biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical readouts and in vivo model, single lab\",\n      \"pmids\": [\"38379270\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ILKAP knockdown reduces PGAM1 expression and suppresses glycolysis (measured by extracellular acidification rate); restoring PGAM1 in ILKAP-knockdown cells rescues proliferation and invasion, placing PGAM1 downstream of ILKAP in metabolic reprogramming.\",\n      \"method\": \"siRNA knockdown, RNA sequencing, PGAM1 rescue overexpression, extracellular acidification rate measurement, xenograft model\",\n      \"journal\": \"Frontiers of medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis rescue experiment with transcriptomic and metabolic readouts, single lab\",\n      \"pmids\": [\"41454076\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ILKAP is a PP2C-family serine/threonine phosphatase that localizes predominantly to the nucleus (via an importin-dependent NLS) and also to the cytoplasm; it directly binds and inhibits ILK1 in a catalysis-dependent manner, selectively suppressing GSK3β (but not AKT) phosphorylation to dampen Wnt/Tcf signaling and cyclin D1 expression, while in the nucleus it dephosphorylates and inactivates RSK2, HIF-1α, and (in some contexts) stabilizes β-catenin by dephosphorylating its regulators GSK3β and CK1; its protein level is regulated by MAEL-driven lysosomal degradation, and loss of ILKAP activates pro-survival kinases (ILK, AKT, RSK, DNA-PK) to confer resistance to genotoxic stresses.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ILKAP is a PP2C-family serine/threonine phosphatase that functions as a negative regulator of integrin-linked kinase (ILK) signaling and a broader hub controlling pro-survival kinase pathways and Wnt-driven gene expression [#0, #2]. It was first identified as a catalysis-independent binding partner of ILK1 that, when catalytically active, selectively inhibits ECM- and growth-factor-stimulated ILK kinase activity without affecting Raf-1 [#0, #1]. Downstream, active ILKAP selectively blocks ILK-dependent GSK3\\u03b2 Ser9 phosphorylation while sparing AKT Ser473, and endogenous loss-of-function by siRNA mirrors this selectivity, defining the ILK\\u2013GSK3\\u03b2 axis as its principal target [#2, #4]. Through this axis ILKAP suppresses Tcf/Lef-dependent transcription and cyclin D1 expression, arresting cells in G1 and limiting anchorage-independent growth [#3, #5]. ILKAP is predominantly nuclear, imported via an N-terminal NLS (residues 71\\u201386, with Lys-78/Arg-79 critical) that binds importin \\u03b11/\\u03b13/\\u03b15 [#8], and it also controls CRM1-dependent nuclear export of ILK [#6]. In the nucleus it binds and dephosphorylates additional substrates including RSK2 and HIF-1\\u03b1 to promote apoptosis [#9, #13], and it binds phosphopeptide substrates of PP2C\\u03b4 such as p38, ATM, Chk1, Chk2, and RSK2 [#7]. ILKAP loss broadly activates pro-survival kinases (ILK, AKT, RSK, DNA-PK), conferring resistance to genotoxic and chemotherapeutic stress [#10, #11], and its protein level is lowered by MAEL-driven lysosomal degradation [#12]. In hepatocellular carcinoma ILKAP can instead stabilize \\u03b2-catenin by dephosphorylating GSK3\\u03b2 and CK1 and bridging TCF4\\u2013\\u03b2-catenin to enhance Wnt targets [#14], and it supports glycolytic reprogramming via PGAM1 [#15].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established that ILKAP physically associates with ILK1 and acts as a phosphatase that selectively suppresses ILK signaling, defining its core function as a negative regulator of ILK rather than a general phosphatase.\",\n      \"evidence\": \"Yeast two-hybrid, co-precipitation, and conditional expression with immune-complex kinase assays plus an H154D catalytic-dead control in HEK293 cells\",\n      \"pmids\": [\"11331582\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct dephosphorylation of ILK or an intermediate not biochemically resolved\", \"Binding shown to be catalysis-independent but functional inhibition catalysis-dependent — coupling mechanism unexplained\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defined downstream selectivity by showing ILKAP blocks ILK\\u2192GSK3\\u03b2 Ser9 phosphorylation and Tcf/Lef transactivation but spares AKT, placing it specifically on the Wnt/GSK3\\u03b2 branch.\",\n      \"evidence\": \"Conditional expression with phosphorylation assays, TOPFlash reporter, and active-site/paralog (PP2C\\u03b1) controls\",\n      \"pmids\": [\"11331582\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether GSK3\\u03b2 is a direct ILKAP substrate or an indirect consequence of ILK inhibition not distinguished\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Confirmed via endogenous loss-of-function that ILKAP physiologically targets the ILK\\u2013GSK3\\u03b2 axis and links its activity to cell-cycle and growth control.\",\n      \"evidence\": \"siRNA knockdown with phosphorylation assays, cyclin D1 readout, cell-cycle and soft-agar assays, and ILK rescue in LNCaP cells\",\n      \"pmids\": [\"14990992\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cyclin D1 regulation inferred through ILK\\u2013GSK3\\u03b2; alternative inputs not excluded\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Extended ILKAP function to spatial control of ILK by showing it promotes CRM1-dependent nuclear export of ILK, coupling its regulation to DNA synthesis.\",\n      \"evidence\": \"Live-cell imaging, nuclear fractionation, leptomycin B treatment, and DNA synthesis assays in keratinocytes\",\n      \"pmids\": [\"18635968\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which ILKAP enhances CRM1 export unresolved\", \"Single cell-type context\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Characterized ILKAP substrate-binding preferences, showing phospho-dependent recognition of PP2C\\u03b4 substrates and implicating it in DNA-damage and stress kinase signaling.\",\n      \"evidence\": \"Solid-phase phosphopeptide affinity pull-downs (p38, ATM, Chk1, Chk2, RSK2) from cell lysates\",\n      \"pmids\": [\"22348942\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding affinity does not establish catalytic dephosphorylation of these substrates in cells\", \"Flanking-context determinants only partially mapped\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Localized ILKAP to the nucleus via a defined importin-binding NLS and identified nuclear RSK2 as a substrate whose inhibition drives apoptosis.\",\n      \"evidence\": \"NLS deletion/point mutagenesis, immunofluorescence, fractionation, importin co-IP, plus RSK2 kinase and apoptosis assays\",\n      \"pmids\": [\"23329845\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether nuclear vs cytoplasmic pools have distinct substrate repertoires not dissected\", \"RSK2 dephosphorylation site not mapped\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Implicated ILKAP in DNA-damage survival signaling by showing it is required for radiation-induced DNA-PK activation in a p53-dependent manner.\",\n      \"evidence\": \"siRNA knockdown with \\u03b3H2AX/53BP1 foci, phospho-DNA-PK blots, and clonogenic survival in GBM cells\",\n      \"pmids\": [\"26460618\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect effect on DNA-PK phosphorylation unresolved\", \"p53-dependence mechanism not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Positioned ILKAP as a multi-kinase regulatory hub whose loss confers chemoresistance by simultaneously activating RSK, ILK, and AKT.\",\n      \"evidence\": \"siRNA knockdown, phospho-Western blots, viability/apoptosis assays, and combined pharmacological kinase inhibition in ovarian cancer cells\",\n      \"pmids\": [\"27065457\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which kinase dephosphorylations are direct not established\", \"Single tumor context\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identified MAEL-driven lysosomal degradation as a mechanism controlling ILKAP protein level and its substrate phosphorylation in tumors.\",\n      \"evidence\": \"Co-expression/silencing, lysosome inhibitors, substrate phospho-blots, xenografts, and adenoviral ILKAP rescue\",\n      \"pmids\": [\"29371914\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular route of lysosomal targeting (e.g. direct MAEL interaction) not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Added HIF-1\\u03b1 as a nuclear ILKAP substrate, linking ILKAP to hypoxic apoptosis via HIF-1\\u03b1\\u2013p53 interaction.\",\n      \"evidence\": \"Co-IP, HRE luciferase reporter, overexpression/shRNA, and viability assays under hypoxia\",\n      \"pmids\": [\"29742494\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"HIF-1\\u03b1 dephosphorylation site not identified\", \"Single-lab functional model\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed a context-dependent pro-Wnt role in hepatocellular carcinoma where ILKAP stabilizes \\u03b2-catenin and bridges TCF4\\u2013\\u03b2-catenin, contrasting with its earlier Wnt-suppressive activity.\",\n      \"evidence\": \"Co-IP, phospho/ubiquitination blots, immunofluorescence, luciferase reporter, and zebrafish xenograft metastasis assays\",\n      \"pmids\": [\"38379270\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reconciliation with the earlier GSK3\\u03b2/Tcf-suppressive model not addressed\", \"Direct dephosphorylation of CK1 vs GSK3\\u03b2 priority unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected ILKAP to metabolic reprogramming by placing PGAM1-dependent glycolysis downstream of ILKAP for proliferation and invasion.\",\n      \"evidence\": \"siRNA knockdown, RNA-seq, ECAR measurement, and PGAM1 rescue in xenografts\",\n      \"pmids\": [\"41454076\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking ILKAP phosphatase activity to PGAM1 expression unknown\", \"Direct vs transcriptional control unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ILKAP's context determines whether it suppresses or promotes Wnt/\\u03b2-catenin signaling, and the structural basis coupling its catalysis-independent ILK binding to catalysis-dependent inhibition, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the ILKAP\\u2013ILK complex\", \"Direct catalytic substrates vs indirect effects not systematically separated\", \"Determinants of opposite Wnt outcomes across tumor types unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 9, 13, 14]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [2, 4, 9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [8, 9, 14]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [8, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 2, 3, 4]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [5, 9]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"ILK\", \"RSK2\", \"HIF1A\", \"CTNNB1\", \"TCF4\", \"KPNA2\", \"MAEL\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}