{"gene":"BUD13","run_date":"2026-06-09T22:02:45","timeline":{"discoveries":[{"year":2019,"finding":"BUD13 acts as an RNA-binding protein that binds to a specific retained intron in Irf7 pre-mRNA and promotes successful splicing, thereby antagonizing intron retention; BUD13 deficiency increases intron retention at a subset of introns sharing characteristics with the Irf7 intron, reduces mature Irf7 transcript and protein levels, and consequently dampens the type I interferon response, impairing macrophage resistance to VSV infection.","method":"BUD13 knockdown with RNA-seq (global intron retention analysis), BUD13 RNA cross-linking (CLIP), mature transcript/protein quantification, viral infection assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal RNA-binding evidence (CLIP + KD), multiple orthogonal readouts (IR, transcript, protein, functional phenotype), single lab but comprehensive mechanistic dissection","pmids":["30639243"],"is_preprint":false},{"year":2022,"finding":"BUD13 loss-of-function (via a homozygous nonsense variant causing alternative splicing to a truncated isoform) in human patients leads to elevated global intron retention, a global reduction of spliceosomal proteins, and nuclear morphology defects (multiple nuclear invaginations) in dermal fibroblasts; overexpression of either BUD13 isoform normalized nuclear morphology, placing BUD13 in the retention and splicing (RES) complex.","method":"Exome sequencing of patients, RNA sequencing, proteomics, immunoblotting, immunostaining, electron microscopy, overexpression rescue assay","journal":"Genetics in medicine","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (RNA-seq, proteomics, EM, rescue), human patient fibroblasts, single lab","pmids":["35670808"],"is_preprint":false},{"year":2023,"finding":"BUD13 functions as an endogenous inhibitor of the E3 ubiquitin ligase Fbw7 by stabilizing Fbw7's oncogenic substrates; cancer-associated BUD13 mutations R156C and R230Q evade RSK3-mediated phosphorylation, enhance oncogenicity, and interfere with Fbw7–Cul1 complex formation, thereby promoting colon cancer growth. BUD13 regulation is also critical in the mTOR inhibition response.","method":"Algorithm-based somatic mutation analysis, validation of phosphorylation evasion (RSK3 kinase assays), Fbw7–Cul1 co-immunoprecipitation, oncogenicity assays in colon cancer models","journal":"The Journal of experimental medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for complex disruption, kinase assay, functional oncogenicity data; single lab, abstract-level detail limits tier assessment","pmids":["37382881"],"is_preprint":false},{"year":2022,"finding":"In glioblastoma cells, METTL3-mediated m6A methylation stabilizes BUD13 mRNA and upregulates BUD13 expression; BUD13 in turn stabilizes CDK12 mRNA, leading to CDK12-mediated phosphorylation of MBNL1, which promotes vasculogenic mimicry formation.","method":"m6A methylation assay, mRNA stability assay, knockdown/overexpression functional studies, subcutaneous tumor xenograft model","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multiple functional readouts (VM, mRNA stability, phosphorylation) and in vivo confirmation, but primarily KD/OE with limited biochemical reconstitution; single lab","pmids":["36463205"],"is_preprint":false},{"year":2020,"finding":"BUD13 binds to the lncRNA DBH-AS1 and stabilizes FN1 mRNA; DBH-AS1 recruits BUD13 to mediate FN1 expression, forming a DBH-AS1/BUD13/FN1 regulatory axis that promotes proliferation, migration, and invasion of DLBCL cells.","method":"RNA immunoprecipitation (RIP), RNA pulldown, mRNA stability assay, rescue/loss-of-function experiments","journal":"Cell biology international","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method type (RIP/pulldown), no independent replication; lncRNA study but BUD13 protein mechanism directly tested","pmids":["32091157"],"is_preprint":false},{"year":2021,"finding":"BUD13 is identified as a component of the retention and splicing (RES) complex, and rare loss-of-function variants in BUD13 co-segregate with specific language impairment (SLI) in humans; loss-of-function mutations in BUD13 in an animal model caused a profound neural phenotype.","method":"Whole-exome sequencing, Sanger sequencing validation, co-segregation analysis, animal model loss-of-function","journal":"Brain sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — human genetic + animal model convergence, multiple families/individuals, but mechanistic detail is limited in the abstract","pmids":["35053791"],"is_preprint":false},{"year":2024,"finding":"In sepsis-associated acute kidney injury models, circ_001653 recruits BUD13 to activate the KEAP1/NRF2/HO-1 signaling pathway, thereby modulating apoptosis, inflammation, and oxidative stress in renal tubular epithelial cells.","method":"RIP, gain/loss-of-function assays, in vitro (LPS-stimulated HK-2 cells) and in vivo (CLP rat) models, subcellular fractionation/FISH for localization","journal":"Journal of inflammation","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanism inferred from BUD13 recruitment by circRNA with pathway readout, limited biochemical characterization of BUD13's direct role","pmids":["39289683"],"is_preprint":false},{"year":2023,"finding":"BUD13 is recruited by lncRNA RNASEH1-AS1 to stabilize ANXA2 mRNA, activating the Wnt/β-catenin pathway and promoting colorectal cancer progression; CBP-mediated H3K27ac drives RNASEH1-AS1 expression upstream of this axis.","method":"ChIP, RIP, RNA pulldown, nucleoplasmic separation/FISH, mRNA stability assay, functional cancer cell assays","journal":"Neoplasma","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, RIP/pulldown evidence for BUD13 recruitment, no independent replication","pmids":["38053379"],"is_preprint":false}],"current_model":"BUD13 is a component of the retention and splicing (RES) complex that functions as an RNA-binding protein to antagonize intron retention at a defined subset of pre-mRNAs (most clearly demonstrated at Irf7), thereby promoting productive splicing and mature transcript output; it also stabilizes select mRNAs (e.g., CDK12, FN1, ANXA2) through recruitment by non-coding RNAs, acts as an endogenous inhibitor of the Fbw7–Cul1 ubiquitin ligase complex, and is subject to regulation by m6A methylation (METTL3) and RSK3-mediated phosphorylation, with cancer-associated mutations at phosphorylation-recognition motifs (R156C, R230Q) conferring gain-of-oncogenic function by disrupting Fbw7 activity."},"narrative":{"mechanistic_narrative":"BUD13 is an RNA-binding component of the retention and splicing (RES) complex that promotes productive pre-mRNA splicing by antagonizing intron retention at a defined subset of introns, most clearly demonstrated at Irf7, where its loss reduces mature transcript and protein output and dampens the type I interferon response, impairing macrophage antiviral resistance [PMID:30639243, PMID:35670808]. Consistent with this role, human BUD13 loss-of-function elevates global intron retention, reduces spliceosomal protein levels, and produces nuclear morphology defects that are rescued by re-expression of BUD13 [PMID:35670808]. Beyond splicing, BUD13 acts as an endogenous inhibitor of the Fbw7–Cul1 ubiquitin ligase by stabilizing Fbw7 oncogenic substrates and interfering with Fbw7–Cul1 complex formation, a function regulated by RSK3-mediated phosphorylation; cancer-associated mutations (R156C, R230Q) evade this phosphorylation and confer gain-of-oncogenic function in colon cancer [PMID:37382881]. BUD13 is itself subject to m6A regulation by METTL3 and is recruited by various non-coding RNAs to stabilize target mRNAs in tumor contexts [PMID:36463205]. Loss-of-function BUD13 variants co-segregate with specific language impairment in humans, with a corresponding neural phenotype in an animal model [PMID:35053791].","teleology":[{"year":2019,"claim":"Established that BUD13 is a sequence-context-selective RNA-binding factor that resolves intron retention, linking its splicing activity to a concrete physiological output (innate antiviral immunity).","evidence":"BUD13 CLIP plus knockdown with global intron-retention RNA-seq, transcript/protein quantification, and VSV infection assay in macrophages","pmids":["30639243"],"confidence":"High","gaps":["Does not define the full set of BUD13-dependent introns or the sequence determinant of selectivity","RES-complex partner requirements for intron resolution not dissected"]},{"year":2021,"claim":"Connected BUD13 to the RES complex and to a human neurodevelopmental phenotype, extending its relevance from cell biology to organism-level function.","evidence":"Whole-exome sequencing with co-segregation analysis in families and an animal loss-of-function model","pmids":["35053791"],"confidence":"Medium","gaps":["Mechanistic link between splicing defects and the neural phenotype not established","Abstract-level mechanistic detail"]},{"year":2022,"claim":"Showed that human BUD13 loss-of-function causes global splicing failure, spliceosomal protein depletion, and nuclear structural defects, confirming its RES-complex role in patient cells.","evidence":"Patient exome sequencing, RNA-seq, proteomics, electron microscopy, and overexpression rescue in dermal fibroblasts","pmids":["35670808"],"confidence":"High","gaps":["Causal chain from splicing loss to nuclear invaginations not resolved","Single-lab patient cohort"]},{"year":2022,"claim":"Identified a regulatory and effector axis in which BUD13 is stabilized by METTL3 m6A methylation and in turn stabilizes downstream mRNA targets, implicating BUD13 in mRNA stability control beyond splicing.","evidence":"m6A and mRNA stability assays with knockdown/overexpression and xenograft model in glioblastoma","pmids":["36463205"],"confidence":"Medium","gaps":["Direct biochemical reconstitution of BUD13-mediated mRNA stabilization lacking","Whether stabilization requires the RES complex unknown"]},{"year":2023,"claim":"Revealed a non-splicing role for BUD13 as an endogenous inhibitor of the Fbw7–Cul1 ligase, and showed how cancer-associated mutations convert it into an oncogenic driver by evading RSK3 phosphorylation.","evidence":"Somatic mutation analysis, RSK3 kinase assays, Fbw7–Cul1 co-immunoprecipitation, and oncogenicity assays in colon cancer models","pmids":["37382881"],"confidence":"Medium","gaps":["Co-IP for complex disruption without reciprocal/structural validation","How phosphorylation status controls Fbw7 binding not mechanistically defined"]},{"year":2023,"claim":"Extended the mRNA-stabilization model to additional non-coding-RNA-recruited contexts, framing BUD13 as a recruitable mRNA-stabilizing factor in cancer.","evidence":"ChIP, RIP, RNA pulldown, FISH, and mRNA stability assays in colorectal cancer cells","pmids":["38053379"],"confidence":"Low","gaps":["RIP/pulldown without independent replication","Direct binding of BUD13 to target mRNA versus indirect recruitment unresolved"]},{"year":2024,"claim":"Reported circRNA-mediated recruitment of BUD13 to the KEAP1/NRF2/HO-1 pathway in kidney injury, suggesting context-dependent roles in oxidative-stress signaling.","evidence":"RIP, gain/loss-of-function assays, FISH, in LPS-stimulated HK-2 cells and CLP rat models","pmids":["39289683"],"confidence":"Low","gaps":["BUD13's direct biochemical role in the pathway not characterized","Single lab, mechanism inferred from recruitment"]},{"year":null,"claim":"How BUD13's splicing/RES-complex activity mechanistically relates to its reported mRNA-stabilization and Fbw7-inhibitory functions remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model linking nuclear splicing role to cytoplasmic/non-coding-RNA-recruited stabilization","Structural basis of RES-complex incorporation and Fbw7 binding undetermined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,4,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1]}],"complexes":["RES complex"],"partners":["FBXW7","CUL1","RSK3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BRD0","full_name":"BUD13 homolog","aliases":[],"length_aa":619,"mass_kda":70.5,"function":"Involved in pre-mRNA splicing as component of the activated spliceosome. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9BRD0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/BUD13","classification":"Common Essential","n_dependent_lines":933,"n_total_lines":1208,"dependency_fraction":0.7723509933774835},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CPSF6","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/BUD13","total_profiled":1310},"omim":[{"mim_id":"621123","title":"ACHALASIA-PROGEROID SYNDROME; ACHPS","url":"https://www.omim.org/entry/621123"},{"mim_id":"620691","title":"BUD13 HOMOLOG; BUD13","url":"https://www.omim.org/entry/620691"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/BUD13"},"hgnc":{"alias_symbol":["MGC13125","fSAP71","Cwc26"],"prev_symbol":[]},"alphafold":{"accession":"Q9BRD0","domains":[{"cath_id":"-","chopping":"462-521","consensus_level":"medium","plddt":86.7165,"start":462,"end":521}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BRD0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BRD0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BRD0-F1-predicted_aligned_error_v6.png","plddt_mean":59.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=BUD13","jax_strain_url":"https://www.jax.org/strain/search?query=BUD13"},"sequence":{"accession":"Q9BRD0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BRD0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BRD0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BRD0"}},"corpus_meta":[{"pmid":"27827461","id":"PMC_27827461","title":"Association and interaction of APOA5, BUD13, CETP, LIPA and health-related behavior with metabolic syndrome in a Taiwanese population.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27827461","citation_count":49,"is_preprint":false},{"pmid":"30639243","id":"PMC_30639243","title":"BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7.","date":"2019","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30639243","citation_count":40,"is_preprint":false},{"pmid":"24780069","id":"PMC_24780069","title":"Association of the variants in the BUD13-ZNF259 genes and the risk of hyperlipidaemia.","date":"2014","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/24780069","citation_count":38,"is_preprint":false},{"pmid":"24989072","id":"PMC_24989072","title":"Association between the MLX interacting protein-like, BUD13 homolog and zinc finger protein 259 gene polymorphisms and serum lipid levels.","date":"2014","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/24989072","citation_count":25,"is_preprint":false},{"pmid":"32091157","id":"PMC_32091157","title":"Long non-coding RNA DBH-AS1 promotes cancer progression in diffuse large B-cell lymphoma by targeting FN1 via RNA-binding protein BUD13.","date":"2020","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/32091157","citation_count":25,"is_preprint":false},{"pmid":"34861864","id":"PMC_34861864","title":"CircSERPINA3 regulates SERPINA3-mediated apoptosis, autophagy and aerobic glycolysis of prostate cancer cells by competitively binding to MiR-653-5p and recruiting BUD13.","date":"2021","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34861864","citation_count":22,"is_preprint":false},{"pmid":"26397108","id":"PMC_26397108","title":"Effects of Polymorphisms in APOA4-APOA5-ZNF259-BUD13 Gene Cluster on Plasma Levels of Triglycerides and Risk of Coronary Heart Disease in a Chinese Han Population.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26397108","citation_count":20,"is_preprint":false},{"pmid":"36463205","id":"PMC_36463205","title":"The mechanism of BUD13 m6A methylation mediated MBNL1-phosphorylation by CDK12 regulating the vasculogenic mimicry in glioblastoma cells.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/36463205","citation_count":19,"is_preprint":false},{"pmid":"28245265","id":"PMC_28245265","title":"Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28245265","citation_count":18,"is_preprint":false},{"pmid":"35053791","id":"PMC_35053791","title":"Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex.","date":"2021","source":"Brain sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35053791","citation_count":16,"is_preprint":false},{"pmid":"31165758","id":"PMC_31165758","title":"Association of BUD13-ZNF259-APOA5-APOA1-SIK3 cluster polymorphism in 11q23.3 and structure of APOA5 with increased plasma triglyceride levels in a Korean population.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31165758","citation_count":15,"is_preprint":false},{"pmid":"33986338","id":"PMC_33986338","title":"Kernel machine SNP set analysis finds the association of BUD13, ZPR1, and APOA5 variants with metabolic syndrome in Tehran Cardio-metabolic Genetics Study.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33986338","citation_count":13,"is_preprint":false},{"pmid":"30631647","id":"PMC_30631647","title":"Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern.","date":"2019","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/30631647","citation_count":12,"is_preprint":false},{"pmid":"39289683","id":"PMC_39289683","title":"Circ_001653 alleviates sepsis associated-acute kidney injury by recruiting BUD13 to regulate KEAP1/NRF2/HO-1 signaling pathway.","date":"2024","source":"Journal of inflammation (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/39289683","citation_count":10,"is_preprint":false},{"pmid":"26885234","id":"PMC_26885234","title":"Association study of BUD13-ZNF259 gene rs964184 polymorphism and hemorrhagic stroke risk.","date":"2015","source":"International journal of clinical and experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26885234","citation_count":8,"is_preprint":false},{"pmid":"31181149","id":"PMC_31181149","title":"Interaction of polymorphisms in APOA4-APOA5-ZPR1-BUD13 gene cluster and sleep duration on 5-year lipid changes in middle aged and older Chinese.","date":"2019","source":"Sleep","url":"https://pubmed.ncbi.nlm.nih.gov/31181149","citation_count":8,"is_preprint":false},{"pmid":"35670808","id":"PMC_35670808","title":"Alternative splicing of BUD13 determines the severity of a developmental disorder with lipodystrophy and progeroid features.","date":"2022","source":"Genetics in medicine : official journal of the American College of Medical Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35670808","citation_count":5,"is_preprint":false},{"pmid":"25900265","id":"PMC_25900265","title":"Differential Lipid Response to Statins Is Associated With Variants in the BUD13-APOA5 Gene Region.","date":"2015","source":"Journal of cardiovascular pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/25900265","citation_count":5,"is_preprint":false},{"pmid":"37382881","id":"PMC_37382881","title":"Somatic gain-of-function mutations in BUD13 promote oncogenesis by disrupting Fbw7 function.","date":"2023","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37382881","citation_count":3,"is_preprint":false},{"pmid":"37641415","id":"PMC_37641415","title":"Regularized Machine Learning Models for Prediction of Metabolic Syndrome Using GCKR, APOA5, and BUD13 Gene Variants: Tehran Cardiometabolic Genetic Study.","date":"2023","source":"Cell journal","url":"https://pubmed.ncbi.nlm.nih.gov/37641415","citation_count":2,"is_preprint":false},{"pmid":"40665476","id":"PMC_40665476","title":"Genome-wide study links cardiometabolic factors to cognition via APOA4-APOA5-ZPR1-BUD13 and other loci in rural Indians.","date":"2025","source":"Alzheimer's & dementia : the journal of the Alzheimer's Association","url":"https://pubmed.ncbi.nlm.nih.gov/40665476","citation_count":1,"is_preprint":false},{"pmid":"38053379","id":"PMC_38053379","title":"RNASEH1-AS1 induced by H3K27ac stabilizes ANXA2 mRNA to promote the progression of colorectal cancer through recruiting BUD13.","date":"2023","source":"Neoplasma","url":"https://pubmed.ncbi.nlm.nih.gov/38053379","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14095,"output_tokens":2165,"usd":0.03738,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9224,"output_tokens":2530,"usd":0.054685,"stage2_stop_reason":"end_turn"},"total_usd":0.092065,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"BUD13 acts as an RNA-binding protein that binds to a specific retained intron in Irf7 pre-mRNA and promotes successful splicing, thereby antagonizing intron retention; BUD13 deficiency increases intron retention at a subset of introns sharing characteristics with the Irf7 intron, reduces mature Irf7 transcript and protein levels, and consequently dampens the type I interferon response, impairing macrophage resistance to VSV infection.\",\n      \"method\": \"BUD13 knockdown with RNA-seq (global intron retention analysis), BUD13 RNA cross-linking (CLIP), mature transcript/protein quantification, viral infection assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal RNA-binding evidence (CLIP + KD), multiple orthogonal readouts (IR, transcript, protein, functional phenotype), single lab but comprehensive mechanistic dissection\",\n      \"pmids\": [\"30639243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"BUD13 loss-of-function (via a homozygous nonsense variant causing alternative splicing to a truncated isoform) in human patients leads to elevated global intron retention, a global reduction of spliceosomal proteins, and nuclear morphology defects (multiple nuclear invaginations) in dermal fibroblasts; overexpression of either BUD13 isoform normalized nuclear morphology, placing BUD13 in the retention and splicing (RES) complex.\",\n      \"method\": \"Exome sequencing of patients, RNA sequencing, proteomics, immunoblotting, immunostaining, electron microscopy, overexpression rescue assay\",\n      \"journal\": \"Genetics in medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (RNA-seq, proteomics, EM, rescue), human patient fibroblasts, single lab\",\n      \"pmids\": [\"35670808\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"BUD13 functions as an endogenous inhibitor of the E3 ubiquitin ligase Fbw7 by stabilizing Fbw7's oncogenic substrates; cancer-associated BUD13 mutations R156C and R230Q evade RSK3-mediated phosphorylation, enhance oncogenicity, and interfere with Fbw7–Cul1 complex formation, thereby promoting colon cancer growth. BUD13 regulation is also critical in the mTOR inhibition response.\",\n      \"method\": \"Algorithm-based somatic mutation analysis, validation of phosphorylation evasion (RSK3 kinase assays), Fbw7–Cul1 co-immunoprecipitation, oncogenicity assays in colon cancer models\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for complex disruption, kinase assay, functional oncogenicity data; single lab, abstract-level detail limits tier assessment\",\n      \"pmids\": [\"37382881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In glioblastoma cells, METTL3-mediated m6A methylation stabilizes BUD13 mRNA and upregulates BUD13 expression; BUD13 in turn stabilizes CDK12 mRNA, leading to CDK12-mediated phosphorylation of MBNL1, which promotes vasculogenic mimicry formation.\",\n      \"method\": \"m6A methylation assay, mRNA stability assay, knockdown/overexpression functional studies, subcutaneous tumor xenograft model\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple functional readouts (VM, mRNA stability, phosphorylation) and in vivo confirmation, but primarily KD/OE with limited biochemical reconstitution; single lab\",\n      \"pmids\": [\"36463205\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"BUD13 binds to the lncRNA DBH-AS1 and stabilizes FN1 mRNA; DBH-AS1 recruits BUD13 to mediate FN1 expression, forming a DBH-AS1/BUD13/FN1 regulatory axis that promotes proliferation, migration, and invasion of DLBCL cells.\",\n      \"method\": \"RNA immunoprecipitation (RIP), RNA pulldown, mRNA stability assay, rescue/loss-of-function experiments\",\n      \"journal\": \"Cell biology international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method type (RIP/pulldown), no independent replication; lncRNA study but BUD13 protein mechanism directly tested\",\n      \"pmids\": [\"32091157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"BUD13 is identified as a component of the retention and splicing (RES) complex, and rare loss-of-function variants in BUD13 co-segregate with specific language impairment (SLI) in humans; loss-of-function mutations in BUD13 in an animal model caused a profound neural phenotype.\",\n      \"method\": \"Whole-exome sequencing, Sanger sequencing validation, co-segregation analysis, animal model loss-of-function\",\n      \"journal\": \"Brain sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — human genetic + animal model convergence, multiple families/individuals, but mechanistic detail is limited in the abstract\",\n      \"pmids\": [\"35053791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In sepsis-associated acute kidney injury models, circ_001653 recruits BUD13 to activate the KEAP1/NRF2/HO-1 signaling pathway, thereby modulating apoptosis, inflammation, and oxidative stress in renal tubular epithelial cells.\",\n      \"method\": \"RIP, gain/loss-of-function assays, in vitro (LPS-stimulated HK-2 cells) and in vivo (CLP rat) models, subcellular fractionation/FISH for localization\",\n      \"journal\": \"Journal of inflammation\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanism inferred from BUD13 recruitment by circRNA with pathway readout, limited biochemical characterization of BUD13's direct role\",\n      \"pmids\": [\"39289683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"BUD13 is recruited by lncRNA RNASEH1-AS1 to stabilize ANXA2 mRNA, activating the Wnt/β-catenin pathway and promoting colorectal cancer progression; CBP-mediated H3K27ac drives RNASEH1-AS1 expression upstream of this axis.\",\n      \"method\": \"ChIP, RIP, RNA pulldown, nucleoplasmic separation/FISH, mRNA stability assay, functional cancer cell assays\",\n      \"journal\": \"Neoplasma\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, RIP/pulldown evidence for BUD13 recruitment, no independent replication\",\n      \"pmids\": [\"38053379\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"BUD13 is a component of the retention and splicing (RES) complex that functions as an RNA-binding protein to antagonize intron retention at a defined subset of pre-mRNAs (most clearly demonstrated at Irf7), thereby promoting productive splicing and mature transcript output; it also stabilizes select mRNAs (e.g., CDK12, FN1, ANXA2) through recruitment by non-coding RNAs, acts as an endogenous inhibitor of the Fbw7–Cul1 ubiquitin ligase complex, and is subject to regulation by m6A methylation (METTL3) and RSK3-mediated phosphorylation, with cancer-associated mutations at phosphorylation-recognition motifs (R156C, R230Q) conferring gain-of-oncogenic function by disrupting Fbw7 activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"BUD13 is an RNA-binding component of the retention and splicing (RES) complex that promotes productive pre-mRNA splicing by antagonizing intron retention at a defined subset of introns, most clearly demonstrated at Irf7, where its loss reduces mature transcript and protein output and dampens the type I interferon response, impairing macrophage antiviral resistance [#0, #1]. Consistent with this role, human BUD13 loss-of-function elevates global intron retention, reduces spliceosomal protein levels, and produces nuclear morphology defects that are rescued by re-expression of BUD13 [#1]. Beyond splicing, BUD13 acts as an endogenous inhibitor of the Fbw7\\u2013Cul1 ubiquitin ligase by stabilizing Fbw7 oncogenic substrates and interfering with Fbw7\\u2013Cul1 complex formation, a function regulated by RSK3-mediated phosphorylation; cancer-associated mutations (R156C, R230Q) evade this phosphorylation and confer gain-of-oncogenic function in colon cancer [#2]. BUD13 is itself subject to m6A regulation by METTL3 and is recruited by various non-coding RNAs to stabilize target mRNAs in tumor contexts [#3]. Loss-of-function BUD13 variants co-segregate with specific language impairment in humans, with a corresponding neural phenotype in an animal model [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Established that BUD13 is a sequence-context-selective RNA-binding factor that resolves intron retention, linking its splicing activity to a concrete physiological output (innate antiviral immunity).\",\n      \"evidence\": \"BUD13 CLIP plus knockdown with global intron-retention RNA-seq, transcript/protein quantification, and VSV infection assay in macrophages\",\n      \"pmids\": [\"30639243\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define the full set of BUD13-dependent introns or the sequence determinant of selectivity\", \"RES-complex partner requirements for intron resolution not dissected\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connected BUD13 to the RES complex and to a human neurodevelopmental phenotype, extending its relevance from cell biology to organism-level function.\",\n      \"evidence\": \"Whole-exome sequencing with co-segregation analysis in families and an animal loss-of-function model\",\n      \"pmids\": [\"35053791\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic link between splicing defects and the neural phenotype not established\", \"Abstract-level mechanistic detail\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed that human BUD13 loss-of-function causes global splicing failure, spliceosomal protein depletion, and nuclear structural defects, confirming its RES-complex role in patient cells.\",\n      \"evidence\": \"Patient exome sequencing, RNA-seq, proteomics, electron microscopy, and overexpression rescue in dermal fibroblasts\",\n      \"pmids\": [\"35670808\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Causal chain from splicing loss to nuclear invaginations not resolved\", \"Single-lab patient cohort\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified a regulatory and effector axis in which BUD13 is stabilized by METTL3 m6A methylation and in turn stabilizes downstream mRNA targets, implicating BUD13 in mRNA stability control beyond splicing.\",\n      \"evidence\": \"m6A and mRNA stability assays with knockdown/overexpression and xenograft model in glioblastoma\",\n      \"pmids\": [\"36463205\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical reconstitution of BUD13-mediated mRNA stabilization lacking\", \"Whether stabilization requires the RES complex unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed a non-splicing role for BUD13 as an endogenous inhibitor of the Fbw7\\u2013Cul1 ligase, and showed how cancer-associated mutations convert it into an oncogenic driver by evading RSK3 phosphorylation.\",\n      \"evidence\": \"Somatic mutation analysis, RSK3 kinase assays, Fbw7\\u2013Cul1 co-immunoprecipitation, and oncogenicity assays in colon cancer models\",\n      \"pmids\": [\"37382881\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Co-IP for complex disruption without reciprocal/structural validation\", \"How phosphorylation status controls Fbw7 binding not mechanistically defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extended the mRNA-stabilization model to additional non-coding-RNA-recruited contexts, framing BUD13 as a recruitable mRNA-stabilizing factor in cancer.\",\n      \"evidence\": \"ChIP, RIP, RNA pulldown, FISH, and mRNA stability assays in colorectal cancer cells\",\n      \"pmids\": [\"38053379\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"RIP/pulldown without independent replication\", \"Direct binding of BUD13 to target mRNA versus indirect recruitment unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Reported circRNA-mediated recruitment of BUD13 to the KEAP1/NRF2/HO-1 pathway in kidney injury, suggesting context-dependent roles in oxidative-stress signaling.\",\n      \"evidence\": \"RIP, gain/loss-of-function assays, FISH, in LPS-stimulated HK-2 cells and CLP rat models\",\n      \"pmids\": [\"39289683\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"BUD13's direct biochemical role in the pathway not characterized\", \"Single lab, mechanism inferred from recruitment\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How BUD13's splicing/RES-complex activity mechanistically relates to its reported mRNA-stabilization and Fbw7-inhibitory functions remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model linking nuclear splicing role to cytoplasmic/non-coding-RNA-recruited stabilization\", \"Structural basis of RES-complex incorporation and Fbw7 binding undetermined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 4, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"RES complex\"],\n    \"partners\": [\"FBXW7\", \"CUL1\", \"RSK3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":5,"faith_pct":80.0}}