{"gene":"PRP4K","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2018,"finding":"PRP4K phosphorylates Yki/YAP in the nucleus at a subset of Wts/Lats1/2 sites, inhibiting Yki/YAP binding to the Scalloped/TEAD transcription factor and promoting CRM1-dependent nuclear export, thereby restricting Hippo pathway target gene expression.","method":"Drosophila genetics (PRP4K gain- and loss-of-function), phosphorylation assays, co-immunoprecipitation, epistasis analysis of Yki-driven tissue overgrowth","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (in vivo genetics, biochemical phosphorylation assays, Co-IP, nuclear export assays), replicated in both Drosophila and mammalian (breast cancer) contexts","pmids":["29695716"],"is_preprint":false},{"year":2017,"finding":"PRP4K localizes not only to the nucleus but also to the cytoplasm at late endosomes; depletion of PRP4K reduces EGFR degradation following cell detachment from the ECM, leading to sustained growth factor signaling and anoikis resistance.","method":"shRNA knockdown, subcellular fractionation/immunofluorescence localization, EGFR trafficking assays, zebrafish xenotransplantation model, mouse ovarian cancer metastasis model","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (localization, trafficking assay, in vivo models) in a single lab","pmids":["28892043"],"is_preprint":false},{"year":2015,"finding":"PRP4K is a component of the U5 snRNP and regulates the spindle assembly checkpoint (SAC) in response to microtubule-targeting drugs; its expression is positively regulated by HER2 signaling, and knockdown reduces taxane sensitivity in breast and ovarian cancer cells.","method":"Co-immunoprecipitation (U5 snRNP association), shRNA knockdown, drug sensitivity assays, correlation with HER2 status in patient tumors","journal":"Cell Cycle","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for complex membership, functional KD with defined cellular phenotype, single lab","pmids":["25602630"],"is_preprint":false},{"year":2015,"finding":"Estrogen receptor alpha (ESR1) signaling directly regulates PRP4K gene and protein expression; ESR1 overexpression increases PRP4K levels in ER-negative cells, ESR1 knockdown reduces PRP4K in ER+ cells, and 4-hydroxytamoxifen treatment dose-dependently decreases PRP4K protein expression correlating with reduced taxane sensitivity.","method":"ESR1 overexpression and shRNA knockdown, 4-OHT treatment, western blot/qRT-PCR, drug sensitivity assays","journal":"Experimental Cell Research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gain- and loss-of-function of ESR1 with defined PRP4K output, multiple cell lines, single lab","pmids":["26712520"],"is_preprint":false},{"year":2022,"finding":"During spliceosomal assembly, PRP4K interacts with and phosphorylates PRPF6 and PRPF31 to facilitate formation of the spliceosome B complex.","method":"Review citing fission yeast and mammalian biochemical studies (interaction and phosphorylation assays)","journal":"Frontiers in Genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — cited as established from prior biochemical work; review summary with no new primary data, but reporting replicated findings from the field","pmids":["35281802"],"is_preprint":false},{"year":2021,"finding":"Induction of EMT by WNT-5a/TGF-β1 reduces PRP4K transcript levels, whereas depletion of eIF3e reduces PRP4K translation; reduced PRP4K after eIF3e depletion correlates with increased YAP nuclear localization and activity, which is reversed by exogenous PRP4K overexpression, placing PRP4K downstream of eIF3e in YAP regulation.","method":"shRNA knockdown of eIF3e, WNT-5a/TGF-β1 treatment to induce EMT, qRT-PCR, western blot, YAP localization assays, rescue by PRP4K overexpression","journal":"FASEB Journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis via rescue experiment, multiple orthogonal readouts, single lab","pmids":["34674320"],"is_preprint":false},{"year":2025,"finding":"PRP4K loss causes mis-splicing and reduced expression of the ESCRT-III gene CHMP4B (and its Dictyostelium ortholog vps32), impairing autophagosome-lysosome fusion; re-expression of CHMP4B or Vps32 cDNA rescues autophagosome-lysosome fusion in PRP4K-deficient human cells and amoebae, defining a PRP4K–CHMP4B/vps32 splicing circuit that regulates autophagy.","method":"PRP4K knockout in Dictyostelium discoideum, shRNA/KO in human cell lines, RNA splicing analysis, autophagosome-lysosome fusion assays, cDNA rescue experiments","journal":"Cell Reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO in two organisms, RNA splicing readout, functional rescue with cDNA, multiple orthogonal methods","pmids":["40531620"],"is_preprint":false},{"year":2025,"finding":"YAPer-ORF (a small protein encoded by LINC01315) localizes to the nucleus and competes with YAP to bind PRP4K, thereby hindering PRP4K-mediated phosphorylation of YAP, promoting YAP nuclear retention and transcription of CCND1.","method":"Co-immunoprecipitation (YAPer-ORF–PRP4K interaction), competition binding assay, YAP phosphorylation assay, nuclear localization analysis, CCND1 expression assay","journal":"Cell Death and Differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for binding, phosphorylation assay showing reduced YAP phosphorylation, functional readout (CCND1, nuclear retention), single lab","pmids":["39962243"],"is_preprint":false},{"year":2023,"finding":"PRP4K-mediated phosphorylation of a conserved serine residue in the nuclear export signal (NES) of Yki is essential for the interaction between Yki and CRM1, driving Yki nuclear export; this phosphorylation does not affect Yki binding to Scalloped (Sd). Bacterial infection upregulates PRP4K expression, promoting Yki nuclear-to-cytoplasmic translocation and modulation of antimicrobial peptide transcription via Cactus.","method":"RNAi of PRP4K and CRM1 in crab hemocytes, phosphorylation site mutagenesis, co-immunoprecipitation (Yki–CRM1, Yki–Sd), bacterial challenge assay, subcellular localization imaging","journal":"Journal of Immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutagenesis of phosphorylation site plus Co-IP in an invertebrate (crab) ortholog context, multiple orthogonal readouts, single lab","pmids":["37154687"],"is_preprint":false},{"year":2026,"finding":"PRPF4B interacts with the RNA-binding protein TIA1; knockdown of PRPF4B promotes expression of a specific TIA1 splice variant that inhibits NF-κB activity, thereby suppressing HCC cell proliferation. PRPF4B knockdown also induces ROS accumulation, DNA damage, and G2/M arrest associated with increased CDC2 phosphorylation, elevated γ-H2AX, and downregulation of CDC25C and cyclin B1.","method":"Co-immunoprecipitation (PRPF4B–TIA1 interaction), shRNA knockdown, alternative splicing analysis, NF-κB reporter/activity assay, cell cycle analysis, ROS/DNA damage assays","journal":"Cellular Signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for interaction, splicing analysis, NF-κB pathway readout, multiple cellular assays, single lab","pmids":["41932413"],"is_preprint":false},{"year":2013,"finding":"Knockdown of PRPF4B (PRP4K) accelerates the G1/S transition and promotes cell growth in hepatocellular carcinoma cell lines; ectopic expression of PRPF4B abolishes the pro-growth phenotypes caused by miR-371-5p overexpression, demonstrating that PRPF4B functions as a cell cycle regulator downstream of miR-371-5p.","method":"shRNA knockdown, miRNA overexpression/inhibition, rescue by PRPF4B re-expression, cell cycle analysis, in vivo tumor xenograft","journal":"Cancer Letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic rescue experiment placing PRPF4B downstream of miR-371-5p in cell cycle control, multiple methods, single lab","pmids":["23466643"],"is_preprint":false}],"current_model":"PRP4K (PRPF4B) is a dual-localized nuclear/cytoplasmic kinase that, in the nucleus, phosphorylates YAP/Yki at Lats1/2 consensus sites to block TEAD/Sd binding and drive CRM1-dependent YAP nuclear export, while also phosphorylating the spliceosomal proteins PRPF6 and PRPF31 as part of the U5 snRNP to facilitate spliceosome B complex assembly; its splicing function extends to regulation of CHMP4B/vps32 pre-mRNA processing, which controls autophagosome–lysosome fusion, and it interacts with TIA1 to modulate alternative splicing of NF-κB pathway components; at the cytoplasm/late endosome, PRP4K supports EGFR lysosomal degradation to enforce anoikis sensitivity, and its expression is regulated upstream by HER2 signaling and estrogen receptor alpha, placing it at the intersection of spliceosomal biology, Hippo/YAP signaling, EGFR trafficking, and autophagy."},"narrative":{"mechanistic_narrative":"PRP4K (PRPF4B) is a dual-function serine kinase that operates both within the spliceosome and as a regulator of Hippo/YAP signaling, linking pre-mRNA processing to growth control [PMID:29695716, PMID:35281802, PMID:40531620]. As a component of the U5 snRNP, it phosphorylates the spliceosomal proteins PRPF6 and PRPF31 to facilitate assembly of the spliceosome B complex [PMID:35281802], and through its splicing activity it controls processing of specific transcripts including the ESCRT-III gene CHMP4B, whose proper splicing is required for autophagosome–lysosome fusion [PMID:40531620]. In the nucleus PRP4K phosphorylates YAP/Yki at a subset of Lats1/2 consensus sites and at a conserved serine within the YAP/Yki nuclear export signal; this blocks TEAD/Scalloped binding and drives CRM1-dependent nuclear export, thereby restricting Hippo target gene expression [PMID:29695716, PMID:37154687]. This kinase activity is antagonized by competitive binders such as the LINC01315-encoded YAPer-ORF, which displaces YAP from PRP4K to promote YAP nuclear retention and CCND1 transcription [PMID:39962243]. Beyond the nucleus, PRP4K localizes to late endosomes where it supports EGFR lysosomal degradation to enforce anoikis sensitivity [PMID:28892043], and it interacts with the RNA-binding protein TIA1 to modulate alternative splicing affecting NF-κB activity [PMID:41932413]. PRP4K expression is set by upstream inputs including HER2 signaling, estrogen receptor alpha, eIF3e-dependent translation, and miR-371-5p, positioning it as a node coupling these pathways to cell cycle progression and drug sensitivity [PMID:25602630, PMID:26712520, PMID:34674320, PMID:23466643].","teleology":[{"year":2013,"claim":"Established that PRPF4B acts as a tumor-suppressive cell cycle regulator, answering whether its loss has growth consequences.","evidence":"shRNA knockdown, miR-371-5p overexpression with PRPF4B rescue, cell cycle analysis and xenograft in hepatocellular carcinoma cells","pmids":["23466643"],"confidence":"Medium","gaps":["Did not define the molecular activity (splicing vs kinase) responsible for G1/S control","No direct substrate identified"]},{"year":2015,"claim":"Placed PRP4K within the U5 snRNP and linked it to spindle assembly checkpoint function and taxane sensitivity downstream of HER2, connecting splicing machinery membership to a chemotherapy-relevant phenotype.","evidence":"Co-IP for U5 snRNP association, shRNA knockdown, drug sensitivity assays, correlation with HER2 status in tumors","pmids":["25602630"],"confidence":"Medium","gaps":["Mechanism connecting splicing role to SAC unclear","Direct phosphorylation substrates within U5 snRNP not defined here"]},{"year":2015,"claim":"Identified estrogen receptor alpha as an upstream transcriptional regulator of PRP4K, explaining how hormone receptor status modulates PRP4K levels and taxane response.","evidence":"ESR1 gain/loss-of-function, 4-OHT treatment, western blot/qRT-PCR, drug sensitivity assays across cell lines","pmids":["26712520"],"confidence":"Medium","gaps":["Whether ESR1 binds the PRP4K promoter directly not shown","Did not connect expression change to a specific PRP4K molecular function"]},{"year":2017,"claim":"Revealed a cytoplasmic, late-endosomal pool of PRP4K supporting EGFR lysosomal degradation, expanding its role beyond the nucleus to receptor trafficking and anoikis control.","evidence":"shRNA knockdown, subcellular fractionation/IF, EGFR trafficking assays, zebrafish xenograft and mouse ovarian cancer metastasis models","pmids":["28892043"],"confidence":"Medium","gaps":["Kinase substrate at the endosome not identified","Mechanism by which PRP4K reaches late endosomes unknown"]},{"year":2018,"claim":"Defined PRP4K as a direct YAP/Yki kinase that restricts Hippo signaling by blocking TEAD binding and promoting nuclear export, establishing a new arm of YAP regulation.","evidence":"Drosophila gain/loss-of-function genetics, phosphorylation assays, Co-IP, nuclear export assays, validated in mammalian breast cancer cells","pmids":["29695716"],"confidence":"High","gaps":["Did not resolve which specific serines are phosphorylated for export vs TEAD blockade","Relationship to canonical Lats1/2 not fully delineated"]},{"year":2021,"claim":"Positioned PRP4K downstream of eIF3e-dependent translation and EMT signaling in YAP control, showing its levels are set translationally to tune YAP activity.","evidence":"eIF3e knockdown, WNT-5a/TGF-β1 EMT induction, YAP localization assays, rescue by PRP4K overexpression","pmids":["34674320"],"confidence":"Medium","gaps":["Direct mechanism of eIF3e selectivity for PRP4K mRNA not shown","In vivo relevance untested"]},{"year":2023,"claim":"Pinpointed phosphorylation of a conserved NES serine as the molecular trigger for Yki–CRM1 interaction and export, separating the export mechanism from TEAD binding, and tied PRP4K to antimicrobial immune signaling.","evidence":"RNAi of PRP4K/CRM1 in crab hemocytes, phosphosite mutagenesis, Co-IP (Yki–CRM1, Yki–Sd), bacterial challenge","pmids":["37154687"],"confidence":"Medium","gaps":["Conservation of this exact NES mechanism in human YAP not directly demonstrated","Invertebrate ortholog context"]},{"year":2025,"claim":"Demonstrated that PRP4K controls autophagy through splicing of the ESCRT-III gene CHMP4B/vps32, defining a concrete splicing-target circuit linking the kinase to autophagosome–lysosome fusion.","evidence":"PRP4K KO in Dictyostelium and human cells, RNA splicing analysis, autophagosome-lysosome fusion assays, cDNA rescue","pmids":["40531620"],"confidence":"High","gaps":["Whether kinase activity or scaffolding drives CHMP4B mis-splicing not separated","Other autophagy-relevant splicing targets not catalogued"]},{"year":2025,"claim":"Identified YAPer-ORF as a competitive inhibitor of PRP4K–YAP binding, showing PRP4K's YAP-suppressing activity is itself regulated by a small protein to drive proliferation.","evidence":"Co-IP, competition binding assay, YAP phosphorylation and nuclear localization assays, CCND1 readout","pmids":["39962243"],"confidence":"Medium","gaps":["Structural basis of competition not resolved","Single-lab finding without reciprocal in vivo validation"]},{"year":2026,"claim":"Linked PRPF4B to TIA1-dependent alternative splicing controlling NF-κB activity and to genome-stability/cell-cycle phenotypes, broadening its splicing regulatory repertoire.","evidence":"Co-IP (PRPF4B–TIA1), shRNA knockdown, splicing analysis, NF-κB reporter, ROS/DNA damage and cell cycle assays in HCC cells","pmids":["41932413"],"confidence":"Medium","gaps":["Whether TIA1 splice variant switch is a direct PRP4B catalytic effect unclear","Mechanism linking PRP4B loss to DNA damage not established"]},{"year":null,"claim":"How PRP4K coordinates its spliceosomal kinase activity with its distinct nuclear YAP-export and cytoplasmic EGFR-trafficking roles, and what governs its partitioning among these compartments, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model distinguishing substrate recognition across roles","Determinants of nuclear vs late-endosomal localization unknown","Full substrate repertoire uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,4,8]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[2,6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1,7]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[2,4,6]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[6]}],"complexes":["U5 snRNP"],"partners":["YAP1","PRPF6","PRPF31","CRM1","TIA1","EGFR"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q13523","full_name":"Serine/threonine-protein kinase PRP4 homolog","aliases":["PRP4 kinase","PRP4 pre-mRNA-processing factor 4 homolog"],"length_aa":1007,"mass_kda":117.0,"function":"Serine/threonine kinase involved in spliceosomal assembly as well as mitosis and signaling regulation (PubMed:10799319, PubMed:12077342, PubMed:17513757, PubMed:17998396). Connects chromatin mediated regulation of transcription and pre-mRNA splicing (PubMed:12077342). During spliceosomal assembly, interacts with and phosphorylates PRPF6 and PRPF31, components of the U4/U6-U5 tri-small nuclear ribonucleoprotein (snRNP), to facilitate the formation of the spliceosome B complex. Plays a role in regulating transcription and the spindle assembly checkpoint (SAC) (PubMed:20118938). Associates with U5 snRNP and NCOR1 deacetylase complexes which may allow a coordination of pre-mRNA splicing with chromatin remodeling events involved in transcriptional regulation (PubMed:12077342). Associates and probably phosphorylates SMARCA4 and NCOR1 (PubMed:12077342). Phosphorylates SRSF1 (PubMed:11418604). Associates with kinetochores during mitosis and is necessary for recruitment and maintenance of the checkpoint proteins such as MAD1L1 and MAD12L1 at the kinetochores (PubMed:17998396). Phosphorylates and regulates the activity of the transcription factors such as ELK1 and KLF13 (PubMed:10799319, PubMed:17513757). Phosphorylates nuclear YAP1 and WWTR1/TAZ which induces nuclear exclusion and regulates Hippo signaling pathway, involved in tissue growth control (PubMed:29695716)","subcellular_location":"Nucleus; Chromosome, centromere, kinetochore","url":"https://www.uniprot.org/uniprotkb/Q13523/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PRP4K","classification":"Common Essential","n_dependent_lines":724,"n_total_lines":1208,"dependency_fraction":0.5993377483443708},"opencell":{"profiled":true,"resolved_as":"PRPF4B","ensg_id":"ENSG00000112739","cell_line_id":"CID001252","localizations":[{"compartment":"chromatin","grade":3},{"compartment":"nuclear_punctae","grade":2}],"interactors":[{"gene":"TRA2B","stoichiometry":10.0},{"gene":"EFTUD2","stoichiometry":10.0},{"gene":"NCBP1","stoichiometry":10.0},{"gene":"SF3B2","stoichiometry":10.0},{"gene":"CHTOP","stoichiometry":10.0},{"gene":"LSM7","stoichiometry":10.0},{"gene":"PRPF19","stoichiometry":10.0},{"gene":"SNRNP40;DKFZP434D199","stoichiometry":10.0},{"gene":"SRRT","stoichiometry":10.0},{"gene":"LSM5","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID001252","total_profiled":1310},"omim":[{"mim_id":"607235","title":"MAS1 ONCOGENE-LIKE; MAS1L","url":"https://www.omim.org/entry/607235"},{"mim_id":"602338","title":"PRE-mRNA-PROCESSING FACTOR KINASE PRP4K; PRP4K","url":"https://www.omim.org/entry/602338"}],"hpa":{"profiled":true,"resolved_as":"PRPF4B","reliability":"Supported","locations":[{"location":"Nuclear speckles","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PRPF4B"},"hgnc":{"alias_symbol":["Prp4","PR4H","KIAA0536","Prp4B"],"prev_symbol":["PRPF4B"]},"alphafold":{"accession":"Q13523","domains":[{"cath_id":"3.30.200.20","chopping":"669-745_752-769","consensus_level":"medium","plddt":90.6373,"start":669,"end":769},{"cath_id":"1.10.510.10","chopping":"770-1007","consensus_level":"medium","plddt":92.5822,"start":770,"end":1007}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13523","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13523-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13523-F1-predicted_aligned_error_v6.png","plddt_mean":60.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PRP4K","jax_strain_url":"https://www.jax.org/strain/search?query=PRP4K"},"sequence":{"accession":"Q13523","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13523.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13523/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13523"}},"corpus_meta":[{"pmid":"29695716","id":"PMC_29695716","title":"Regulation of Yki/Yap subcellular localization and Hpo signaling by a nuclear kinase PRP4K.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29695716","citation_count":42,"is_preprint":false},{"pmid":"23466643","id":"PMC_23466643","title":"miR-371-5p down-regulates pre mRNA processing factor 4 homolog B (PRPF4B) and facilitates the G1/S transition in human hepatocellular carcinoma cells.","date":"2013","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/23466643","citation_count":33,"is_preprint":false},{"pmid":"28892043","id":"PMC_28892043","title":"Loss of PRP4K drives anoikis resistance in part by dysregulation of epidermal growth factor receptor endosomal trafficking.","date":"2017","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/28892043","citation_count":26,"is_preprint":false},{"pmid":"25602630","id":"PMC_25602630","title":"PRP4K is a HER2-regulated modifier of taxane sensitivity.","date":"2015","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/25602630","citation_count":19,"is_preprint":false},{"pmid":"26712520","id":"PMC_26712520","title":"Estrogen receptor alpha (ESR1)-signaling regulates the expression of the taxane-response biomarker PRP4K.","date":"2015","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/26712520","citation_count":8,"is_preprint":false},{"pmid":"35281802","id":"PMC_35281802","title":"Tinker, Tailor, Tumour Suppressor: The Many Functions of PRP4K.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35281802","citation_count":7,"is_preprint":false},{"pmid":"34674320","id":"PMC_34674320","title":"Haploinsufficient tumor suppressor PRP4K is negatively regulated during epithelial-to-mesenchymal transition.","date":"2021","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/34674320","citation_count":6,"is_preprint":false},{"pmid":"39962243","id":"PMC_39962243","title":"The LINC01315-encoded small protein YAPer-ORF competes with PRP4k to hijack YAP signaling to aberrantly promote cell growth.","date":"2025","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/39962243","citation_count":5,"is_preprint":false},{"pmid":"37154687","id":"PMC_37154687","title":"Subcellular Translocation of Yorkie through the PRP4K-CRM1 Axis Regulates Antimicrobial Peptides Transcription and Defense against Bacterial Infection in Crab.","date":"2023","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/37154687","citation_count":5,"is_preprint":false},{"pmid":"40531620","id":"PMC_40531620","title":"The evolutionarily conserved PRP4K-CHMP4B/vps32 splicing circuit regulates autophagy.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/40531620","citation_count":0,"is_preprint":false},{"pmid":"41932413","id":"PMC_41932413","title":"PRPF4B drives hepatocellular carcinoma progression by modulating NF-κB signaling via TIA1-regulated alternative splicing.","date":"2026","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/41932413","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.24.684341","title":"Altiratinib Targets PRP4K in  <i>Theileria annulata</i>  , Disrupting RNA Processing and Inducing Apoptosis in Infected Cells","date":"2025-10-24","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.24.684341","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8450,"output_tokens":3026,"usd":0.03537,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10419,"output_tokens":3634,"usd":0.071472,"stage2_stop_reason":"end_turn"},"total_usd":0.106842,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"PRP4K phosphorylates Yki/YAP in the nucleus at a subset of Wts/Lats1/2 sites, inhibiting Yki/YAP binding to the Scalloped/TEAD transcription factor and promoting CRM1-dependent nuclear export, thereby restricting Hippo pathway target gene expression.\",\n      \"method\": \"Drosophila genetics (PRP4K gain- and loss-of-function), phosphorylation assays, co-immunoprecipitation, epistasis analysis of Yki-driven tissue overgrowth\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (in vivo genetics, biochemical phosphorylation assays, Co-IP, nuclear export assays), replicated in both Drosophila and mammalian (breast cancer) contexts\",\n      \"pmids\": [\"29695716\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PRP4K localizes not only to the nucleus but also to the cytoplasm at late endosomes; depletion of PRP4K reduces EGFR degradation following cell detachment from the ECM, leading to sustained growth factor signaling and anoikis resistance.\",\n      \"method\": \"shRNA knockdown, subcellular fractionation/immunofluorescence localization, EGFR trafficking assays, zebrafish xenotransplantation model, mouse ovarian cancer metastasis model\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (localization, trafficking assay, in vivo models) in a single lab\",\n      \"pmids\": [\"28892043\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PRP4K is a component of the U5 snRNP and regulates the spindle assembly checkpoint (SAC) in response to microtubule-targeting drugs; its expression is positively regulated by HER2 signaling, and knockdown reduces taxane sensitivity in breast and ovarian cancer cells.\",\n      \"method\": \"Co-immunoprecipitation (U5 snRNP association), shRNA knockdown, drug sensitivity assays, correlation with HER2 status in patient tumors\",\n      \"journal\": \"Cell Cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for complex membership, functional KD with defined cellular phenotype, single lab\",\n      \"pmids\": [\"25602630\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Estrogen receptor alpha (ESR1) signaling directly regulates PRP4K gene and protein expression; ESR1 overexpression increases PRP4K levels in ER-negative cells, ESR1 knockdown reduces PRP4K in ER+ cells, and 4-hydroxytamoxifen treatment dose-dependently decreases PRP4K protein expression correlating with reduced taxane sensitivity.\",\n      \"method\": \"ESR1 overexpression and shRNA knockdown, 4-OHT treatment, western blot/qRT-PCR, drug sensitivity assays\",\n      \"journal\": \"Experimental Cell Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gain- and loss-of-function of ESR1 with defined PRP4K output, multiple cell lines, single lab\",\n      \"pmids\": [\"26712520\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"During spliceosomal assembly, PRP4K interacts with and phosphorylates PRPF6 and PRPF31 to facilitate formation of the spliceosome B complex.\",\n      \"method\": \"Review citing fission yeast and mammalian biochemical studies (interaction and phosphorylation assays)\",\n      \"journal\": \"Frontiers in Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — cited as established from prior biochemical work; review summary with no new primary data, but reporting replicated findings from the field\",\n      \"pmids\": [\"35281802\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Induction of EMT by WNT-5a/TGF-β1 reduces PRP4K transcript levels, whereas depletion of eIF3e reduces PRP4K translation; reduced PRP4K after eIF3e depletion correlates with increased YAP nuclear localization and activity, which is reversed by exogenous PRP4K overexpression, placing PRP4K downstream of eIF3e in YAP regulation.\",\n      \"method\": \"shRNA knockdown of eIF3e, WNT-5a/TGF-β1 treatment to induce EMT, qRT-PCR, western blot, YAP localization assays, rescue by PRP4K overexpression\",\n      \"journal\": \"FASEB Journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis via rescue experiment, multiple orthogonal readouts, single lab\",\n      \"pmids\": [\"34674320\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PRP4K loss causes mis-splicing and reduced expression of the ESCRT-III gene CHMP4B (and its Dictyostelium ortholog vps32), impairing autophagosome-lysosome fusion; re-expression of CHMP4B or Vps32 cDNA rescues autophagosome-lysosome fusion in PRP4K-deficient human cells and amoebae, defining a PRP4K–CHMP4B/vps32 splicing circuit that regulates autophagy.\",\n      \"method\": \"PRP4K knockout in Dictyostelium discoideum, shRNA/KO in human cell lines, RNA splicing analysis, autophagosome-lysosome fusion assays, cDNA rescue experiments\",\n      \"journal\": \"Cell Reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO in two organisms, RNA splicing readout, functional rescue with cDNA, multiple orthogonal methods\",\n      \"pmids\": [\"40531620\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"YAPer-ORF (a small protein encoded by LINC01315) localizes to the nucleus and competes with YAP to bind PRP4K, thereby hindering PRP4K-mediated phosphorylation of YAP, promoting YAP nuclear retention and transcription of CCND1.\",\n      \"method\": \"Co-immunoprecipitation (YAPer-ORF–PRP4K interaction), competition binding assay, YAP phosphorylation assay, nuclear localization analysis, CCND1 expression assay\",\n      \"journal\": \"Cell Death and Differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for binding, phosphorylation assay showing reduced YAP phosphorylation, functional readout (CCND1, nuclear retention), single lab\",\n      \"pmids\": [\"39962243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PRP4K-mediated phosphorylation of a conserved serine residue in the nuclear export signal (NES) of Yki is essential for the interaction between Yki and CRM1, driving Yki nuclear export; this phosphorylation does not affect Yki binding to Scalloped (Sd). Bacterial infection upregulates PRP4K expression, promoting Yki nuclear-to-cytoplasmic translocation and modulation of antimicrobial peptide transcription via Cactus.\",\n      \"method\": \"RNAi of PRP4K and CRM1 in crab hemocytes, phosphorylation site mutagenesis, co-immunoprecipitation (Yki–CRM1, Yki–Sd), bacterial challenge assay, subcellular localization imaging\",\n      \"journal\": \"Journal of Immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis of phosphorylation site plus Co-IP in an invertebrate (crab) ortholog context, multiple orthogonal readouts, single lab\",\n      \"pmids\": [\"37154687\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PRPF4B interacts with the RNA-binding protein TIA1; knockdown of PRPF4B promotes expression of a specific TIA1 splice variant that inhibits NF-κB activity, thereby suppressing HCC cell proliferation. PRPF4B knockdown also induces ROS accumulation, DNA damage, and G2/M arrest associated with increased CDC2 phosphorylation, elevated γ-H2AX, and downregulation of CDC25C and cyclin B1.\",\n      \"method\": \"Co-immunoprecipitation (PRPF4B–TIA1 interaction), shRNA knockdown, alternative splicing analysis, NF-κB reporter/activity assay, cell cycle analysis, ROS/DNA damage assays\",\n      \"journal\": \"Cellular Signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for interaction, splicing analysis, NF-κB pathway readout, multiple cellular assays, single lab\",\n      \"pmids\": [\"41932413\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Knockdown of PRPF4B (PRP4K) accelerates the G1/S transition and promotes cell growth in hepatocellular carcinoma cell lines; ectopic expression of PRPF4B abolishes the pro-growth phenotypes caused by miR-371-5p overexpression, demonstrating that PRPF4B functions as a cell cycle regulator downstream of miR-371-5p.\",\n      \"method\": \"shRNA knockdown, miRNA overexpression/inhibition, rescue by PRPF4B re-expression, cell cycle analysis, in vivo tumor xenograft\",\n      \"journal\": \"Cancer Letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic rescue experiment placing PRPF4B downstream of miR-371-5p in cell cycle control, multiple methods, single lab\",\n      \"pmids\": [\"23466643\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PRP4K (PRPF4B) is a dual-localized nuclear/cytoplasmic kinase that, in the nucleus, phosphorylates YAP/Yki at Lats1/2 consensus sites to block TEAD/Sd binding and drive CRM1-dependent YAP nuclear export, while also phosphorylating the spliceosomal proteins PRPF6 and PRPF31 as part of the U5 snRNP to facilitate spliceosome B complex assembly; its splicing function extends to regulation of CHMP4B/vps32 pre-mRNA processing, which controls autophagosome–lysosome fusion, and it interacts with TIA1 to modulate alternative splicing of NF-κB pathway components; at the cytoplasm/late endosome, PRP4K supports EGFR lysosomal degradation to enforce anoikis sensitivity, and its expression is regulated upstream by HER2 signaling and estrogen receptor alpha, placing it at the intersection of spliceosomal biology, Hippo/YAP signaling, EGFR trafficking, and autophagy.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PRP4K (PRPF4B) is a dual-function serine kinase that operates both within the spliceosome and as a regulator of Hippo/YAP signaling, linking pre-mRNA processing to growth control [#0, #4, #6]. As a component of the U5 snRNP, it phosphorylates the spliceosomal proteins PRPF6 and PRPF31 to facilitate assembly of the spliceosome B complex [#4], and through its splicing activity it controls processing of specific transcripts including the ESCRT-III gene CHMP4B, whose proper splicing is required for autophagosome–lysosome fusion [#6]. In the nucleus PRP4K phosphorylates YAP/Yki at a subset of Lats1/2 consensus sites and at a conserved serine within the YAP/Yki nuclear export signal; this blocks TEAD/Scalloped binding and drives CRM1-dependent nuclear export, thereby restricting Hippo target gene expression [#0, #8]. This kinase activity is antagonized by competitive binders such as the LINC01315-encoded YAPer-ORF, which displaces YAP from PRP4K to promote YAP nuclear retention and CCND1 transcription [#7]. Beyond the nucleus, PRP4K localizes to late endosomes where it supports EGFR lysosomal degradation to enforce anoikis sensitivity [#1], and it interacts with the RNA-binding protein TIA1 to modulate alternative splicing affecting NF-κB activity [#9]. PRP4K expression is set by upstream inputs including HER2 signaling, estrogen receptor alpha, eIF3e-dependent translation, and miR-371-5p, positioning it as a node coupling these pathways to cell cycle progression and drug sensitivity [#2, #3, #5, #10].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established that PRPF4B acts as a tumor-suppressive cell cycle regulator, answering whether its loss has growth consequences.\",\n      \"evidence\": \"shRNA knockdown, miR-371-5p overexpression with PRPF4B rescue, cell cycle analysis and xenograft in hepatocellular carcinoma cells\",\n      \"pmids\": [\"23466643\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define the molecular activity (splicing vs kinase) responsible for G1/S control\", \"No direct substrate identified\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Placed PRP4K within the U5 snRNP and linked it to spindle assembly checkpoint function and taxane sensitivity downstream of HER2, connecting splicing machinery membership to a chemotherapy-relevant phenotype.\",\n      \"evidence\": \"Co-IP for U5 snRNP association, shRNA knockdown, drug sensitivity assays, correlation with HER2 status in tumors\",\n      \"pmids\": [\"25602630\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting splicing role to SAC unclear\", \"Direct phosphorylation substrates within U5 snRNP not defined here\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identified estrogen receptor alpha as an upstream transcriptional regulator of PRP4K, explaining how hormone receptor status modulates PRP4K levels and taxane response.\",\n      \"evidence\": \"ESR1 gain/loss-of-function, 4-OHT treatment, western blot/qRT-PCR, drug sensitivity assays across cell lines\",\n      \"pmids\": [\"26712520\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ESR1 binds the PRP4K promoter directly not shown\", \"Did not connect expression change to a specific PRP4K molecular function\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealed a cytoplasmic, late-endosomal pool of PRP4K supporting EGFR lysosomal degradation, expanding its role beyond the nucleus to receptor trafficking and anoikis control.\",\n      \"evidence\": \"shRNA knockdown, subcellular fractionation/IF, EGFR trafficking assays, zebrafish xenograft and mouse ovarian cancer metastasis models\",\n      \"pmids\": [\"28892043\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinase substrate at the endosome not identified\", \"Mechanism by which PRP4K reaches late endosomes unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined PRP4K as a direct YAP/Yki kinase that restricts Hippo signaling by blocking TEAD binding and promoting nuclear export, establishing a new arm of YAP regulation.\",\n      \"evidence\": \"Drosophila gain/loss-of-function genetics, phosphorylation assays, Co-IP, nuclear export assays, validated in mammalian breast cancer cells\",\n      \"pmids\": [\"29695716\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which specific serines are phosphorylated for export vs TEAD blockade\", \"Relationship to canonical Lats1/2 not fully delineated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Positioned PRP4K downstream of eIF3e-dependent translation and EMT signaling in YAP control, showing its levels are set translationally to tune YAP activity.\",\n      \"evidence\": \"eIF3e knockdown, WNT-5a/TGF-β1 EMT induction, YAP localization assays, rescue by PRP4K overexpression\",\n      \"pmids\": [\"34674320\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mechanism of eIF3e selectivity for PRP4K mRNA not shown\", \"In vivo relevance untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Pinpointed phosphorylation of a conserved NES serine as the molecular trigger for Yki–CRM1 interaction and export, separating the export mechanism from TEAD binding, and tied PRP4K to antimicrobial immune signaling.\",\n      \"evidence\": \"RNAi of PRP4K/CRM1 in crab hemocytes, phosphosite mutagenesis, Co-IP (Yki–CRM1, Yki–Sd), bacterial challenge\",\n      \"pmids\": [\"37154687\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Conservation of this exact NES mechanism in human YAP not directly demonstrated\", \"Invertebrate ortholog context\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated that PRP4K controls autophagy through splicing of the ESCRT-III gene CHMP4B/vps32, defining a concrete splicing-target circuit linking the kinase to autophagosome–lysosome fusion.\",\n      \"evidence\": \"PRP4K KO in Dictyostelium and human cells, RNA splicing analysis, autophagosome-lysosome fusion assays, cDNA rescue\",\n      \"pmids\": [\"40531620\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether kinase activity or scaffolding drives CHMP4B mis-splicing not separated\", \"Other autophagy-relevant splicing targets not catalogued\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified YAPer-ORF as a competitive inhibitor of PRP4K–YAP binding, showing PRP4K's YAP-suppressing activity is itself regulated by a small protein to drive proliferation.\",\n      \"evidence\": \"Co-IP, competition binding assay, YAP phosphorylation and nuclear localization assays, CCND1 readout\",\n      \"pmids\": [\"39962243\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of competition not resolved\", \"Single-lab finding without reciprocal in vivo validation\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Linked PRPF4B to TIA1-dependent alternative splicing controlling NF-κB activity and to genome-stability/cell-cycle phenotypes, broadening its splicing regulatory repertoire.\",\n      \"evidence\": \"Co-IP (PRPF4B–TIA1), shRNA knockdown, splicing analysis, NF-κB reporter, ROS/DNA damage and cell cycle assays in HCC cells\",\n      \"pmids\": [\"41932413\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether TIA1 splice variant switch is a direct PRP4B catalytic effect unclear\", \"Mechanism linking PRP4B loss to DNA damage not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PRP4K coordinates its spliceosomal kinase activity with its distinct nuclear YAP-export and cytoplasmic EGFR-trafficking roles, and what governs its partitioning among these compartments, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model distinguishing substrate recognition across roles\", \"Determinants of nuclear vs late-endosomal localization unknown\", \"Full substrate repertoire uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 4, 8]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [2, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 7]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 4, 6]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\n      \"U5 snRNP\"\n    ],\n    \"partners\": [\n      \"YAP1\",\n      \"PRPF6\",\n      \"PRPF31\",\n      \"CRM1\",\n      \"TIA1\",\n      \"EGFR\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}