{"gene":"WBP11","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":1999,"finding":"WBP11 (NpwBP) was identified as a binding partner of the WW-domain protein Npw38 (PQBP1). The WW domain of Npw38 preferentially recognizes a proline-rich PGR motif (PPGPPP surrounded by arginine) present in two regions of WBP11. Co-immunoprecipitation of epitope-tagged proteins in COS7 cells confirmed the interaction, and GFP-fusion/immunostaining showed co-localization in the same subnuclear region. The N-terminal region of WBP11 also binds poly(rG) and G-rich single-stranded DNA.","method":"Co-immunoprecipitation (epitope-tagged proteins in COS7 cells), oligopeptide-immobilized membrane binding analysis, GFP fusion/immunostaining, nucleic acid binding assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and independent binding assays in single lab, multiple orthogonal methods","pmids":["10593949"],"is_preprint":false},{"year":2004,"finding":"WBP11 (SIPP1) was identified as a component of the spliceosome and a direct interactor of protein phosphatase-1 (PP1). WBP11 inhibits PP1 activity, and this inhibitory potency is increased by phosphorylation with protein kinase CK1. Two-hybrid and co-sedimentation analysis revealed two distinct PP1-binding domains in WBP11, with binding involving an RVXF motif. WBP11 localizes exclusively to the nucleus and is enriched in nuclear speckles; the N-terminus contains a nuclear localization signal and the proline-rich C-terminal domain is required for subnuclear targeting to speckles. A WBP11 fragment inhibits splicing catalysis by nuclear extracts independently of PP1 interaction.","method":"Yeast two-hybrid, co-sedimentation, PP1 activity assay, kinase assay (CK1), EGFP localization, nuclear extract splicing assay, domain mapping","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — multiple orthogonal methods (enzymatic assay, yeast two-hybrid, co-sedimentation, in vitro splicing, localization) in single lab","pmids":["14640981"],"is_preprint":false},{"year":2005,"finding":"WBP11 (SIPP1) is a nucleocytoplasmic shuttling protein. Under basal conditions it is largely nuclear, but accumulates in the cytoplasm following UV or X-radiation. Nuclear import is mediated by two nuclear localization signals and can also occur via piggy-back transport with its ligand PQBP1. WBP11 relocates nuclear PP1 to storage sites for splicing factors but does not function as a nuclear targeting subunit of PP1. Nuclear export requires C-terminal residues and proceeds via the CRM1 pathway. WBP11 activates pre-mRNA splicing in intact cells, with splicing activation correlating with its nuclear concentration.","method":"GFP fusion localization, radiation treatment, nuclear export inhibition (CRM1 pathway), co-expression with PQBP1, splicing activation assay in intact cells, domain deletion analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (localization, functional splicing assay, domain mapping, pathway inhibition) in single lab","pmids":["16162498"],"is_preprint":false},{"year":2019,"finding":"WBP11 is required for centriole duplication. Loss of WBP11 causes retention of ~200 introns, including multiple introns in TUBGCP6 (a core component of the γ-TuRC), leading to rapid decline in TUBGCP6 protein levels and consequent centriole duplication failure. Several other splicing factors required for centriole duplication were shown to physically interact with WBP11.","method":"siRNA/shRNA depletion, RNA-seq (intron retention analysis), immunofluorescence (centriole counting), Western blot (TUBGCP6 protein levels), co-immunoprecipitation (splicing factor interactions)","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with specific cellular phenotype, RNA-seq mechanistic link to substrate, protein interaction, replicated across multiple splicing factors","pmids":["31874114"],"is_preprint":false},{"year":2019,"finding":"KIAA1199 binds to WBP11 and regulates E-cadherin and N-cadherin expression via the FGFR4/Wnt/β-catenin and EGFR signaling pathways; ectopic expression of WBP11 blocked the stimulatory effects of KIAA1199 on gastric cancer cell proliferation and migration, placing WBP11 downstream of KIAA1199 in this pathway.","method":"Co-immunoprecipitation (KIAA1199-WBP11 binding), overexpression/knockdown in GC cell lines, in vitro and in vivo migration/proliferation assays","journal":"Oncogene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP with partial functional follow-up; WBP11 role is secondary to the main KIAA1199 story","pmids":["30626935"],"is_preprint":false},{"year":2020,"finding":"Heterozygous loss-of-function of WBP11 in mice (CRISPR-Cas9 null allele) causes congenital malformations (axial skeleton, kidneys, esophagus defects) and embryonic/postnatal lethality; homozygous null embryos die before E8.5, demonstrating WBP11 is essential for early development. This positions WBP11's spliceosomal function as required for organogenesis.","method":"CRISPR-Cas9 null mouse generation, embryo lethal phenotyping, heterozygous phenotype characterization (skeletal/renal/esophageal defects)","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic KO with specific developmental phenotypes, replicated in mouse model consistent with human patient variants","pmids":["33276377"],"is_preprint":false},{"year":2024,"finding":"WBP11 promotes ovarian cancer progression by repressing intron 4 retention of MCM7 pre-mRNA, thereby maintaining MCM7 expression. FOXM1 transcriptionally activates WBP11 by directly binding to its promoter. WBP11 depletion reduces MCM7 protein, and MCM7 inhibition attenuated the malignant effects of WBP11 overexpression, placing WBP11 in a FOXM1→WBP11→MCM7 axis.","method":"RNA-seq/alternative splicing analysis (intron retention), siRNA knockdown, ChIP (FOXM1 binding to WBP11 promoter), in vitro and in vivo proliferation/migration assays, rescue experiments","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA-seq mechanistic link, ChIP for upstream regulator, functional rescue; single lab","pmids":["38561505"],"is_preprint":false},{"year":2025,"finding":"WBP11 N-terminal domain interacts with the RNA recognition motif (RRM) domain of NONO and enhances glycolysis in HCC cells. WBP11 maintains NONO protein stability by competitively inhibiting UFL1-induced UFMylation of NONO at Lys198. Enforced NONO expression rescued the suppression of growth and metastasis caused by WBP11 depletion, demonstrating a WBP11→NONO stability→HCC progression axis.","method":"Co-immunoprecipitation (WBP11-NONO interaction, domain mapping), UFMylation assay (UFL1, Lys198 mutant), glycolysis measurement, siRNA knockdown, in vitro and in vivo rescue experiments","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping, post-translational modification site identified, functional rescue; single lab","pmids":["41184530"],"is_preprint":false}],"current_model":"WBP11 is a nuclear pre-mRNA splicing factor that resides in nuclear speckles and the spliceosome, activates splicing (including by suppressing intron retention in targets such as TUBGCP6 and MCM7), shuttles between nucleus and cytoplasm via CRM1-dependent export regulated by radiation stress, inhibits protein phosphatase-1 (PP1) through an RVXF-motif interaction whose potency is enhanced by CK1 phosphorylation, interacts with PQBP1/Npw38 via a PGR proline-rich motif, and in non-splicing contexts stabilizes the RNA-binding protein NONO by blocking UFL1-mediated UFMylation at Lys198; haploinsufficiency in mice and humans causes multiple congenital anomalies (cardiac, vertebral, renal, esophageal defects) at least partly through splicing defects in key developmental transcripts."},"narrative":{"mechanistic_narrative":"WBP11 is a nuclear pre-mRNA splicing factor that resides in nuclear speckles and the spliceosome and actively promotes splicing catalysis in intact cells [PMID:14640981, PMID:16162498]. It is built around modular interaction surfaces: a proline-rich PGR motif that is recognized by the WW domain of the splicing-associated protein PQBP1/Npw38, and an RVXF motif through which it directly binds and inhibits protein phosphatase-1 (PP1), an inhibitory activity that is potentiated by CK1 phosphorylation [PMID:10593949, PMID:14640981]. WBP11 carries nuclear localization signals required for nuclear import (and can be imported by piggy-back transport with PQBP1) while its proline-rich C-terminus directs targeting to speckles and mediates CRM1-dependent nuclear export that is triggered by UV or X-radiation, coupling its splicing-activating function to its nuclear concentration [PMID:14640981, PMID:16162498]. Mechanistically, WBP11 suppresses intron retention in specific transcripts: it preserves correct splicing of TUBGCP6 to sustain γ-TuRC integrity and centriole duplication, and represses intron 4 retention of MCM7 to maintain MCM7 protein levels [PMID:31874114, PMID:38561505]. This splicing function is essential for organogenesis, as heterozygous loss-of-function in mice causes congenital axial skeleton, kidney, and esophageal malformations while homozygous loss is embryonic lethal before E8.5 [PMID:33276377]. WBP11 also acts in non-splicing contexts to drive cancer progression, including a FOXM1→WBP11→MCM7 axis in ovarian cancer and stabilization of the RNA-binding protein NONO by competitively blocking UFL1-mediated UFMylation at Lys198 in hepatocellular carcinoma [PMID:38561505, PMID:41184530].","teleology":[{"year":1999,"claim":"Established WBP11's first molecular partnership, defining a proline-rich PGR motif as the docking site for the WW domain of PQBP1/Npw38 and revealing nucleic-acid binding by its N-terminus.","evidence":"Reciprocal Co-IP of epitope-tagged proteins in COS7 cells, oligopeptide membrane binding, GFP co-localization, and poly(rG)/ssDNA binding assays","pmids":["10593949"],"confidence":"Medium","gaps":["Functional consequence of the PQBP1 interaction for splicing not defined","Significance of N-terminal nucleic-acid binding unresolved","Single-lab interaction without independent confirmation"]},{"year":2004,"claim":"Placed WBP11 in the spliceosome and identified it as an RVXF-motif PP1 inhibitor whose potency is tuned by CK1 phosphorylation, while showing a WBP11 fragment can block splicing catalysis independently of PP1.","evidence":"Yeast two-hybrid, co-sedimentation, PP1 activity and CK1 kinase assays, in vitro nuclear extract splicing, EGFP localization and domain mapping","pmids":["14640981"],"confidence":"High","gaps":["Physiological splicing substrates not identified","How PP1 inhibition relates to splicing activation unclear","Mechanism by which the fragment blocks catalysis undefined"]},{"year":2005,"claim":"Resolved WBP11 trafficking, showing it shuttles between nucleus and cytoplasm with CRM1-dependent export induced by radiation, and that its nuclear concentration determines the degree of splicing activation.","evidence":"GFP-fusion localization, radiation treatment, CRM1 export inhibition, PQBP1 co-expression, and splicing activation assays in intact cells with domain deletions","pmids":["16162498"],"confidence":"High","gaps":["Signaling link between radiation stress and export not mapped","Direct splicing targets still unknown at this stage","Whether cytoplasmic relocation has a distinct function unresolved"]},{"year":2019,"claim":"Connected WBP11 splicing activity to a concrete cellular outcome by showing it suppresses intron retention in TUBGCP6 to sustain γ-TuRC and centriole duplication, embedding it in a network of centriole-promoting splicing factors.","evidence":"siRNA/shRNA depletion, RNA-seq intron-retention analysis, centriole immunofluorescence, TUBGCP6 Western blot, and Co-IP of splicing factors","pmids":["31874114"],"confidence":"High","gaps":["How WBP11 selects retained-intron targets unknown","Direct vs indirect role on TUBGCP6 splicing not dissected","Identity of the spliceosomal subcomplex WBP11 acts within unclear"]},{"year":2019,"claim":"Implicated WBP11 in cancer signaling as a downstream effector of KIAA1199 affecting cadherin expression and gastric cancer behavior.","evidence":"Co-IP of KIAA1199-WBP11, overexpression/knockdown in gastric cancer lines, and migration/proliferation assays in vitro and in vivo","pmids":["30626935"],"confidence":"Low","gaps":["Single Co-IP without reciprocal validation; WBP11 role secondary to KIAA1199 narrative","Molecular mechanism linking WBP11 to cadherin pathways undefined","No splicing-based mechanism tested"]},{"year":2020,"claim":"Demonstrated that WBP11 is essential for development in vivo, with heterozygous loss producing congenital malformations and homozygous loss causing early embryonic lethality, tying its splicing function to organogenesis.","evidence":"CRISPR-Cas9 null mouse generation, embryonic lethality phenotyping, and characterization of skeletal/renal/esophageal defects in heterozygotes","pmids":["33276377"],"confidence":"High","gaps":["Specific developmental transcripts mis-spliced in vivo not fully enumerated","Tissue-specific requirements not dissected","Mechanism linking haploinsufficiency to each organ defect incomplete"]},{"year":2024,"claim":"Defined a transcriptional-to-splicing cascade in which FOXM1 activates WBP11, which in turn represses MCM7 intron 4 retention to maintain MCM7 and drive ovarian cancer progression.","evidence":"RNA-seq/splicing analysis, siRNA knockdown, FOXM1 ChIP on the WBP11 promoter, and proliferation/migration plus rescue assays in vitro and in vivo","pmids":["38561505"],"confidence":"Medium","gaps":["Generality of MCM7 intron regulation beyond ovarian cancer untested","Direct binding of WBP11 to MCM7 pre-mRNA not shown","Single-lab axis"]},{"year":2025,"claim":"Revealed a splicing-independent role in which WBP11 stabilizes NONO by competitively blocking UFL1-mediated UFMylation at Lys198, enhancing glycolysis and hepatocellular carcinoma progression.","evidence":"Co-IP with domain mapping (WBP11 N-terminus to NONO RRM), UFMylation assays with UFL1 and a Lys198 mutant, glycolysis measurements, knockdown, and rescue in vitro and in vivo","pmids":["41184530"],"confidence":"Medium","gaps":["Whether NONO stabilization is independent of WBP11's nuclear splicing role unclear","Structural basis of competition with UFL1 unknown","Single-lab axis"]},{"year":null,"claim":"How WBP11 selects its specific intron-retention targets and integrates PP1 inhibition, PQBP1 binding, radiation-regulated shuttling, and its non-splicing protein-stabilization activities into a unified mechanism remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of WBP11 or its spliceosomal complex","Rules governing target intron selection unknown","Relationship between PP1 inhibition and splicing activation undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[2,3,6]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[1,2]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,2,3,6]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[5]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[6,7]}],"complexes":["spliceosome","nuclear speckles"],"partners":["PQBP1","PPP1CA","TUBGCP6","NONO","UFL1","KIAA1199","FOXM1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y2W2","full_name":"WW domain-binding protein 11","aliases":["Npw38-binding protein","NpwBP","SH3 domain-binding protein SNP70","Splicing factor that interacts with PQBP-1 and PP1"],"length_aa":641,"mass_kda":70.0,"function":"Activates pre-mRNA splicing. May inhibit PP1 phosphatase activity","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9Y2W2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/WBP11","classification":"Common Essential","n_dependent_lines":1203,"n_total_lines":1208,"dependency_fraction":0.9958609271523179},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ARF4","stoichiometry":10.0},{"gene":"ATP6AP2","stoichiometry":10.0},{"gene":"XPO1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/WBP11","total_profiled":1310},"omim":[{"mim_id":"619227","title":"VERTEBRAL, CARDIAC, TRACHEOESOPHAGEAL, RENAL, AND LIMB DEFECTS; VCTERL","url":"https://www.omim.org/entry/619227"},{"mim_id":"618083","title":"WW-BINDING PROTEIN 11; WBP11","url":"https://www.omim.org/entry/618083"},{"mim_id":"300463","title":"POLYGLUTAMINE-BINDING PROTEIN 1; PQBP1","url":"https://www.omim.org/entry/300463"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Vesicles","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"},{"location":"Acrosome","reliability":"Additional"},{"location":"Principal piece","reliability":"Additional"},{"location":"End piece","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/WBP11"},"hgnc":{"alias_symbol":["NPWBP","SIPP1","PPP1R165","BUG13"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y2W2","domains":[{"cath_id":"1.20.5","chopping":"14-47","consensus_level":"medium","plddt":93.645,"start":14,"end":47},{"cath_id":"1.20.58","chopping":"49-131","consensus_level":"medium","plddt":92.8167,"start":49,"end":131}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2W2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2W2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2W2-F1-predicted_aligned_error_v6.png","plddt_mean":62.59},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=WBP11","jax_strain_url":"https://www.jax.org/strain/search?query=WBP11"},"sequence":{"accession":"Q9Y2W2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2W2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2W2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2W2"}},"corpus_meta":[{"pmid":"10593949","id":"PMC_10593949","title":"Association of two nuclear proteins, Npw38 and NpwBP, via the interaction between the WW domain and a novel proline-rich motif containing glycine and arginine.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10593949","citation_count":76,"is_preprint":false},{"pmid":"30626935","id":"PMC_30626935","title":"The miR-29c-KIAA1199 axis regulates gastric cancer migration by binding with WBP11 and PTP4A3.","date":"2019","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/30626935","citation_count":61,"is_preprint":false},{"pmid":"14640981","id":"PMC_14640981","title":"SIPP1, a novel pre-mRNA splicing factor and interactor of protein phosphatase-1.","date":"2004","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/14640981","citation_count":51,"is_preprint":false},{"pmid":"16162498","id":"PMC_16162498","title":"Nucleocytoplasmic shuttling of the splicing factor SIPP1.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16162498","citation_count":43,"is_preprint":false},{"pmid":"33276377","id":"PMC_33276377","title":"Heterozygous loss of WBP11 function causes multiple congenital defects in humans and mice.","date":"2020","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33276377","citation_count":24,"is_preprint":false},{"pmid":"38561505","id":"PMC_38561505","title":"The splicing factor WBP11 mediates MCM7 intron retention to promote the malignant progression of ovarian cancer.","date":"2024","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/38561505","citation_count":19,"is_preprint":false},{"pmid":"31874114","id":"PMC_31874114","title":"WBP11 is required for splicing the TUBGCP6 pre-mRNA to promote centriole duplication.","date":"2019","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/31874114","citation_count":18,"is_preprint":false},{"pmid":"41184530","id":"PMC_41184530","title":"WBP11 inhibits UFL1-mediated UFMylation of NONO to drive hepatocellular carcinoma progression.","date":"2025","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/41184530","citation_count":3,"is_preprint":false},{"pmid":"40089178","id":"PMC_40089178","title":"Isolated congenital vertebral anomaly and Sprengel's deformity in a WBP11 pathogenic variant.","date":"2025","source":"European journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40089178","citation_count":3,"is_preprint":false},{"pmid":"41185117","id":"PMC_41185117","title":"A de novo WBP11 Pathogenic Variant in a Fetus With Cystic Brain Malformation and Growth Restriction.","date":"2025","source":"Prenatal diagnosis","url":"https://pubmed.ncbi.nlm.nih.gov/41185117","citation_count":1,"is_preprint":false},{"pmid":"41975533","id":"PMC_41975533","title":"Prenatal and postnatal manifestations of WBP11-related disorder in Chinese patients: expanding the phenotypic and mutational spectrum.","date":"2026","source":"Human genomics","url":"https://pubmed.ncbi.nlm.nih.gov/41975533","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7349,"output_tokens":2596,"usd":0.030493,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9743,"output_tokens":3526,"usd":0.068432,"stage2_stop_reason":"end_turn"},"total_usd":0.098925,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"WBP11 (NpwBP) was identified as a binding partner of the WW-domain protein Npw38 (PQBP1). The WW domain of Npw38 preferentially recognizes a proline-rich PGR motif (PPGPPP surrounded by arginine) present in two regions of WBP11. Co-immunoprecipitation of epitope-tagged proteins in COS7 cells confirmed the interaction, and GFP-fusion/immunostaining showed co-localization in the same subnuclear region. The N-terminal region of WBP11 also binds poly(rG) and G-rich single-stranded DNA.\",\n      \"method\": \"Co-immunoprecipitation (epitope-tagged proteins in COS7 cells), oligopeptide-immobilized membrane binding analysis, GFP fusion/immunostaining, nucleic acid binding assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and independent binding assays in single lab, multiple orthogonal methods\",\n      \"pmids\": [\"10593949\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"WBP11 (SIPP1) was identified as a component of the spliceosome and a direct interactor of protein phosphatase-1 (PP1). WBP11 inhibits PP1 activity, and this inhibitory potency is increased by phosphorylation with protein kinase CK1. Two-hybrid and co-sedimentation analysis revealed two distinct PP1-binding domains in WBP11, with binding involving an RVXF motif. WBP11 localizes exclusively to the nucleus and is enriched in nuclear speckles; the N-terminus contains a nuclear localization signal and the proline-rich C-terminal domain is required for subnuclear targeting to speckles. A WBP11 fragment inhibits splicing catalysis by nuclear extracts independently of PP1 interaction.\",\n      \"method\": \"Yeast two-hybrid, co-sedimentation, PP1 activity assay, kinase assay (CK1), EGFP localization, nuclear extract splicing assay, domain mapping\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — multiple orthogonal methods (enzymatic assay, yeast two-hybrid, co-sedimentation, in vitro splicing, localization) in single lab\",\n      \"pmids\": [\"14640981\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"WBP11 (SIPP1) is a nucleocytoplasmic shuttling protein. Under basal conditions it is largely nuclear, but accumulates in the cytoplasm following UV or X-radiation. Nuclear import is mediated by two nuclear localization signals and can also occur via piggy-back transport with its ligand PQBP1. WBP11 relocates nuclear PP1 to storage sites for splicing factors but does not function as a nuclear targeting subunit of PP1. Nuclear export requires C-terminal residues and proceeds via the CRM1 pathway. WBP11 activates pre-mRNA splicing in intact cells, with splicing activation correlating with its nuclear concentration.\",\n      \"method\": \"GFP fusion localization, radiation treatment, nuclear export inhibition (CRM1 pathway), co-expression with PQBP1, splicing activation assay in intact cells, domain deletion analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (localization, functional splicing assay, domain mapping, pathway inhibition) in single lab\",\n      \"pmids\": [\"16162498\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"WBP11 is required for centriole duplication. Loss of WBP11 causes retention of ~200 introns, including multiple introns in TUBGCP6 (a core component of the γ-TuRC), leading to rapid decline in TUBGCP6 protein levels and consequent centriole duplication failure. Several other splicing factors required for centriole duplication were shown to physically interact with WBP11.\",\n      \"method\": \"siRNA/shRNA depletion, RNA-seq (intron retention analysis), immunofluorescence (centriole counting), Western blot (TUBGCP6 protein levels), co-immunoprecipitation (splicing factor interactions)\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with specific cellular phenotype, RNA-seq mechanistic link to substrate, protein interaction, replicated across multiple splicing factors\",\n      \"pmids\": [\"31874114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"KIAA1199 binds to WBP11 and regulates E-cadherin and N-cadherin expression via the FGFR4/Wnt/β-catenin and EGFR signaling pathways; ectopic expression of WBP11 blocked the stimulatory effects of KIAA1199 on gastric cancer cell proliferation and migration, placing WBP11 downstream of KIAA1199 in this pathway.\",\n      \"method\": \"Co-immunoprecipitation (KIAA1199-WBP11 binding), overexpression/knockdown in GC cell lines, in vitro and in vivo migration/proliferation assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP with partial functional follow-up; WBP11 role is secondary to the main KIAA1199 story\",\n      \"pmids\": [\"30626935\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Heterozygous loss-of-function of WBP11 in mice (CRISPR-Cas9 null allele) causes congenital malformations (axial skeleton, kidneys, esophagus defects) and embryonic/postnatal lethality; homozygous null embryos die before E8.5, demonstrating WBP11 is essential for early development. This positions WBP11's spliceosomal function as required for organogenesis.\",\n      \"method\": \"CRISPR-Cas9 null mouse generation, embryo lethal phenotyping, heterozygous phenotype characterization (skeletal/renal/esophageal defects)\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic KO with specific developmental phenotypes, replicated in mouse model consistent with human patient variants\",\n      \"pmids\": [\"33276377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"WBP11 promotes ovarian cancer progression by repressing intron 4 retention of MCM7 pre-mRNA, thereby maintaining MCM7 expression. FOXM1 transcriptionally activates WBP11 by directly binding to its promoter. WBP11 depletion reduces MCM7 protein, and MCM7 inhibition attenuated the malignant effects of WBP11 overexpression, placing WBP11 in a FOXM1→WBP11→MCM7 axis.\",\n      \"method\": \"RNA-seq/alternative splicing analysis (intron retention), siRNA knockdown, ChIP (FOXM1 binding to WBP11 promoter), in vitro and in vivo proliferation/migration assays, rescue experiments\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA-seq mechanistic link, ChIP for upstream regulator, functional rescue; single lab\",\n      \"pmids\": [\"38561505\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"WBP11 N-terminal domain interacts with the RNA recognition motif (RRM) domain of NONO and enhances glycolysis in HCC cells. WBP11 maintains NONO protein stability by competitively inhibiting UFL1-induced UFMylation of NONO at Lys198. Enforced NONO expression rescued the suppression of growth and metastasis caused by WBP11 depletion, demonstrating a WBP11→NONO stability→HCC progression axis.\",\n      \"method\": \"Co-immunoprecipitation (WBP11-NONO interaction, domain mapping), UFMylation assay (UFL1, Lys198 mutant), glycolysis measurement, siRNA knockdown, in vitro and in vivo rescue experiments\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping, post-translational modification site identified, functional rescue; single lab\",\n      \"pmids\": [\"41184530\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WBP11 is a nuclear pre-mRNA splicing factor that resides in nuclear speckles and the spliceosome, activates splicing (including by suppressing intron retention in targets such as TUBGCP6 and MCM7), shuttles between nucleus and cytoplasm via CRM1-dependent export regulated by radiation stress, inhibits protein phosphatase-1 (PP1) through an RVXF-motif interaction whose potency is enhanced by CK1 phosphorylation, interacts with PQBP1/Npw38 via a PGR proline-rich motif, and in non-splicing contexts stabilizes the RNA-binding protein NONO by blocking UFL1-mediated UFMylation at Lys198; haploinsufficiency in mice and humans causes multiple congenital anomalies (cardiac, vertebral, renal, esophageal defects) at least partly through splicing defects in key developmental transcripts.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"WBP11 is a nuclear pre-mRNA splicing factor that resides in nuclear speckles and the spliceosome and actively promotes splicing catalysis in intact cells [#1, #2]. It is built around modular interaction surfaces: a proline-rich PGR motif that is recognized by the WW domain of the splicing-associated protein PQBP1/Npw38, and an RVXF motif through which it directly binds and inhibits protein phosphatase-1 (PP1), an inhibitory activity that is potentiated by CK1 phosphorylation [#0, #1]. WBP11 carries nuclear localization signals required for nuclear import (and can be imported by piggy-back transport with PQBP1) while its proline-rich C-terminus directs targeting to speckles and mediates CRM1-dependent nuclear export that is triggered by UV or X-radiation, coupling its splicing-activating function to its nuclear concentration [#1, #2]. Mechanistically, WBP11 suppresses intron retention in specific transcripts: it preserves correct splicing of TUBGCP6 to sustain γ-TuRC integrity and centriole duplication, and represses intron 4 retention of MCM7 to maintain MCM7 protein levels [#3, #6]. This splicing function is essential for organogenesis, as heterozygous loss-of-function in mice causes congenital axial skeleton, kidney, and esophageal malformations while homozygous loss is embryonic lethal before E8.5 [#5]. WBP11 also acts in non-splicing contexts to drive cancer progression, including a FOXM1→WBP11→MCM7 axis in ovarian cancer and stabilization of the RNA-binding protein NONO by competitively blocking UFL1-mediated UFMylation at Lys198 in hepatocellular carcinoma [#6, #7].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established WBP11's first molecular partnership, defining a proline-rich PGR motif as the docking site for the WW domain of PQBP1/Npw38 and revealing nucleic-acid binding by its N-terminus.\",\n      \"evidence\": \"Reciprocal Co-IP of epitope-tagged proteins in COS7 cells, oligopeptide membrane binding, GFP co-localization, and poly(rG)/ssDNA binding assays\",\n      \"pmids\": [\"10593949\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the PQBP1 interaction for splicing not defined\", \"Significance of N-terminal nucleic-acid binding unresolved\", \"Single-lab interaction without independent confirmation\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Placed WBP11 in the spliceosome and identified it as an RVXF-motif PP1 inhibitor whose potency is tuned by CK1 phosphorylation, while showing a WBP11 fragment can block splicing catalysis independently of PP1.\",\n      \"evidence\": \"Yeast two-hybrid, co-sedimentation, PP1 activity and CK1 kinase assays, in vitro nuclear extract splicing, EGFP localization and domain mapping\",\n      \"pmids\": [\"14640981\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological splicing substrates not identified\", \"How PP1 inhibition relates to splicing activation unclear\", \"Mechanism by which the fragment blocks catalysis undefined\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Resolved WBP11 trafficking, showing it shuttles between nucleus and cytoplasm with CRM1-dependent export induced by radiation, and that its nuclear concentration determines the degree of splicing activation.\",\n      \"evidence\": \"GFP-fusion localization, radiation treatment, CRM1 export inhibition, PQBP1 co-expression, and splicing activation assays in intact cells with domain deletions\",\n      \"pmids\": [\"16162498\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signaling link between radiation stress and export not mapped\", \"Direct splicing targets still unknown at this stage\", \"Whether cytoplasmic relocation has a distinct function unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Connected WBP11 splicing activity to a concrete cellular outcome by showing it suppresses intron retention in TUBGCP6 to sustain γ-TuRC and centriole duplication, embedding it in a network of centriole-promoting splicing factors.\",\n      \"evidence\": \"siRNA/shRNA depletion, RNA-seq intron-retention analysis, centriole immunofluorescence, TUBGCP6 Western blot, and Co-IP of splicing factors\",\n      \"pmids\": [\"31874114\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How WBP11 selects retained-intron targets unknown\", \"Direct vs indirect role on TUBGCP6 splicing not dissected\", \"Identity of the spliceosomal subcomplex WBP11 acts within unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Implicated WBP11 in cancer signaling as a downstream effector of KIAA1199 affecting cadherin expression and gastric cancer behavior.\",\n      \"evidence\": \"Co-IP of KIAA1199-WBP11, overexpression/knockdown in gastric cancer lines, and migration/proliferation assays in vitro and in vivo\",\n      \"pmids\": [\"30626935\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP without reciprocal validation; WBP11 role secondary to KIAA1199 narrative\", \"Molecular mechanism linking WBP11 to cadherin pathways undefined\", \"No splicing-based mechanism tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrated that WBP11 is essential for development in vivo, with heterozygous loss producing congenital malformations and homozygous loss causing early embryonic lethality, tying its splicing function to organogenesis.\",\n      \"evidence\": \"CRISPR-Cas9 null mouse generation, embryonic lethality phenotyping, and characterization of skeletal/renal/esophageal defects in heterozygotes\",\n      \"pmids\": [\"33276377\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific developmental transcripts mis-spliced in vivo not fully enumerated\", \"Tissue-specific requirements not dissected\", \"Mechanism linking haploinsufficiency to each organ defect incomplete\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined a transcriptional-to-splicing cascade in which FOXM1 activates WBP11, which in turn represses MCM7 intron 4 retention to maintain MCM7 and drive ovarian cancer progression.\",\n      \"evidence\": \"RNA-seq/splicing analysis, siRNA knockdown, FOXM1 ChIP on the WBP11 promoter, and proliferation/migration plus rescue assays in vitro and in vivo\",\n      \"pmids\": [\"38561505\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Generality of MCM7 intron regulation beyond ovarian cancer untested\", \"Direct binding of WBP11 to MCM7 pre-mRNA not shown\", \"Single-lab axis\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed a splicing-independent role in which WBP11 stabilizes NONO by competitively blocking UFL1-mediated UFMylation at Lys198, enhancing glycolysis and hepatocellular carcinoma progression.\",\n      \"evidence\": \"Co-IP with domain mapping (WBP11 N-terminus to NONO RRM), UFMylation assays with UFL1 and a Lys198 mutant, glycolysis measurements, knockdown, and rescue in vitro and in vivo\",\n      \"pmids\": [\"41184530\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether NONO stabilization is independent of WBP11's nuclear splicing role unclear\", \"Structural basis of competition with UFL1 unknown\", \"Single-lab axis\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How WBP11 selects its specific intron-retention targets and integrates PP1 inhibition, PQBP1 binding, radiation-regulated shuttling, and its non-splicing protein-stabilization activities into a unified mechanism remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of WBP11 or its spliceosomal complex\", \"Rules governing target intron selection unknown\", \"Relationship between PP1 inhibition and splicing activation undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [2, 3, 6]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 2, 3, 6]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"complexes\": [\"spliceosome\", \"nuclear speckles\"],\n    \"partners\": [\"PQBP1\", \"PPP1CA\", \"TUBGCP6\", \"NONO\", \"UFL1\", \"KIAA1199\", \"FOXM1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}