{"gene":"FBXO16","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2018,"finding":"FBXO16, as a component of the SCF E3 ubiquitin ligase complex, interacts with β-catenin and mediates its proteasomal degradation in a GSK-3β-independent manner. Specifically, the C-terminal region of FBXO16 targets nuclear β-catenin for K-48 linked poly-ubiquitination, inhibiting TCF4/LEF1-dependent Wnt signaling in glioblastoma cells.","method":"Co-immunoprecipitation, ubiquitination assays, nuclear fractionation, loss-of-function/gain-of-function experiments in GBM cells","journal":"Neoplasia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and ubiquitination assay with K48-linkage specificity, single lab, multiple orthogonal methods","pmids":["30530053"],"is_preprint":false},{"year":2019,"finding":"FBXO16 forms an SCF (SKP1-Cullin1-FBXO16) complex that physically interacts with the C-terminal domain of β-catenin and promotes its K48-linked polyubiquitination and subsequent 26S proteasomal degradation. FBXO16 depletion increases nuclear β-catenin levels, promoting EMT, cell invasion, and tumor growth in breast cancer cells.","method":"Co-immunoprecipitation, in vivo ubiquitination assay, siRNA knockdown with proliferation/invasion readouts, clinical breast cancer sample analysis","journal":"The Journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, ubiquitination assays, and KD phenotype with multiple readouts, single lab","pmids":["30714168"],"is_preprint":false},{"year":2021,"finding":"FBXO16 assembles a canonical SCF ubiquitin ligase complex via its F-box domain and constitutively targets hnRNPL for proteasomal degradation. FBXO16 interacts specifically with the RRM3 domain of hnRNPL through its C-terminal region, and loss of FBXO16 leads to hnRNPL accumulation that activates multiple oncogenic signaling pathways in ovarian cancer.","method":"Co-immunoprecipitation, domain-mapping pulldowns, siRNA knockdown and CRISPR depletion, ubiquitination assay, in vivo tumor growth assay, domain-deletion mutants","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP with domain mapping, in vivo ubiquitination, KO rescue experiments, in vitro and in vivo tumor models, multiple orthogonal methods in single lab","pmids":["34333526"],"is_preprint":false},{"year":2024,"finding":"FBXO16 negatively regulates ULK1 by targeting it for degradation; miR-937-5p (a product of MIR937 amplification) binds the 3' UTR of FBXO16 transcript to suppress FBXO16 expression, thereby relieving FBXO16-mediated degradation of ULK1 and enhancing autophagy and proliferation in high-grade serous ovarian cancer cells.","method":"miRNA target binding assay (3' UTR luciferase), siRNA/CRISPR deletion of MIR937, rescue assays, autophagy flux measurements, cell proliferation assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — 3' UTR binding validated, epistasis rescue confirmed, single lab with multiple orthogonal methods","pmids":["39384743"],"is_preprint":false},{"year":2025,"finding":"Fbxo16 functions as a substrate-recognition receptor for the NF-κB p65 subunit within a PDLIM2-Cullin1-Skp1 ubiquitin ligase complex. Fbxo16 binds p65, promotes its polyubiquitination and proteasomal degradation, suppresses NF-κB transactivation, and Fbxo16 deficiency in dendritic cells results in increased nuclear p65 and enhanced proinflammatory cytokine production. Fbxo16 did not promote degradation of STAT3 or STAT4.","method":"siRNA screen of F-box proteins, Co-immunoprecipitation, ubiquitination assay, Fbxo16 KO dendritic cells with cytokine and nuclear fractionation readouts, STAT3/STAT4 functional assays (negative control)","journal":"Frontiers in immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, in vivo ubiquitination, KO functional readout with multiple orthogonal methods, substrate specificity confirmed by negative controls for STAT3/STAT4","pmids":["40529355"],"is_preprint":false},{"year":2002,"finding":"FBXO16 was identified as a novel human F-box protein encoded by a gene on chromosome 8p12, consisting of 9 exons spanning 67,816 bp of genomic DNA, with 90% amino acid identity to mouse Fbxo16. RT-PCR detected expression in heart, spleen, and colon.","method":"cDNA cloning from human fetal brain library, Northern blot, RT-PCR, genomic mapping","journal":"Molecules and cells","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — initial cloning and expression characterization, replicated by later functional studies confirming F-box protein identity","pmids":["12243353"],"is_preprint":false}],"current_model":"FBXO16 is an F-box protein that functions as the substrate-recognition subunit of SCF (SKP1-Cullin1-FBXO16) E3 ubiquitin ligase complexes, targeting multiple substrates—including nuclear β-catenin, hnRNPL, NF-κB p65, and ULK1—for K48-linked polyubiquitination and 26S proteasomal degradation, thereby suppressing Wnt/β-catenin signaling, oncogenic RNA-binding protein activity, NF-κB-mediated inflammation, and autophagy in a context-dependent manner."},"narrative":{"mechanistic_narrative":"FBXO16 is an F-box protein that serves as the substrate-recognition subunit of SCF (SKP1–Cullin1–FBXO16) E3 ubiquitin ligase complexes, directing diverse substrates toward K48-linked polyubiquitination and 26S proteasomal degradation [PMID:30530053, PMID:34333526]. A recurrent theme across studies is its tumor-suppressive role through control of nuclear signaling pools: its C-terminal region binds nuclear β-catenin and drives its degradation in a GSK-3β-independent manner, restraining TCF4/LEF1-dependent Wnt signaling, with depletion promoting EMT, invasion, and tumor growth [PMID:30530053, PMID:30714168]. FBXO16 also constitutively targets the RNA-binding protein hnRNPL—via its RRM3 domain—for degradation, and its loss leads to hnRNPL accumulation and activation of oncogenic signaling in ovarian cancer [PMID:34333526]. Beyond cancer signaling, FBXO16 acts as the substrate receptor that delivers the NF-κB p65 subunit for ubiquitination, suppressing NF-κB transactivation and proinflammatory cytokine production in dendritic cells, with substrate specificity confirmed by its failure to degrade STAT3 or STAT4 [PMID:40529355]. It additionally limits autophagy by degrading ULK1; this brake is relieved when miR-937-5p represses FBXO16 expression [PMID:39384743]. FBXO16 was originally identified as a human F-box gene on chromosome 8p12 [PMID:12243353].","teleology":[{"year":2002,"claim":"Before any functional role was known, the question was whether FBXO16 was a bona fide F-box gene; cloning established it as a novel human F-box protein with a defined genomic structure and tissue expression.","evidence":"cDNA cloning from a human fetal brain library, Northern blot, RT-PCR, and genomic mapping to chromosome 8p12","pmids":["12243353"],"confidence":"Medium","gaps":["No substrate or biochemical activity assigned at this stage","F-box partner subunits (SKP1/Cullin1) not yet demonstrated"]},{"year":2018,"claim":"The first substrate question—what does FBXO16 ubiquitinate—was answered by showing it targets nuclear β-catenin for K48-linked degradation independently of GSK-3β, defining a tumor-suppressive node in Wnt signaling.","evidence":"Co-IP, K48-specific ubiquitination assays, and nuclear fractionation with loss/gain-of-function in glioblastoma cells","pmids":["30530053"],"confidence":"Medium","gaps":["Mechanism of nuclear targeting/recruitment of FBXO16 to β-catenin unclear","Single-lab finding in one tumor context"]},{"year":2019,"claim":"Extending the β-catenin model, this work confirmed assembly of the SKP1-Cullin1-FBXO16 SCF complex on β-catenin's C-terminal domain and linked its loss to EMT and metastatic phenotypes in breast cancer.","evidence":"Reciprocal Co-IP, in vivo ubiquitination assay, siRNA knockdown with invasion/proliferation readouts, and clinical sample analysis","pmids":["30714168"],"confidence":"Medium","gaps":["Did not resolve whether nuclear vs cytoplasmic β-catenin pools are differentially targeted","Upstream regulation of FBXO16 abundance not addressed"]},{"year":2021,"claim":"The substrate repertoire was broadened beyond β-catenin by demonstrating that FBXO16 constitutively degrades the RNA-binding protein hnRNPL via its RRM3 domain, connecting the ligase to control of oncogenic RNA-processing activity.","evidence":"Reciprocal Co-IP with domain mapping, in vivo ubiquitination, CRISPR/siRNA depletion with KO rescue, and in vitro/in vivo ovarian tumor models","pmids":["34333526"],"confidence":"High","gaps":["Downstream oncogenic pathways activated by hnRNPL not fully delineated","Whether β-catenin and hnRNPL are degraded by the same cellular pool of FBXO16 unknown"]},{"year":2024,"claim":"How FBXO16 itself is suppressed in cancer, and what this releases, was addressed by showing miR-937-5p represses FBXO16 to stabilize ULK1 and enhance autophagy—implicating FBXO16 as an autophagy brake.","evidence":"3' UTR luciferase binding assay, CRISPR deletion of MIR937, rescue and autophagy-flux measurements in high-grade serous ovarian cancer cells","pmids":["39384743"],"confidence":"Medium","gaps":["Direct ubiquitination of ULK1 by an SCF-FBXO16 complex not biochemically mapped here","Single-lab epistasis model"]},{"year":2025,"claim":"A distinct immune role was established by identifying FBXO16 as the p65 substrate receptor within a PDLIM2-Cullin1-Skp1 ligase, with degradation specificity validated against STAT3/STAT4 negative controls, linking it to NF-κB-mediated inflammation.","evidence":"siRNA screen of F-box proteins, Co-IP, ubiquitination assay, and Fbxo16 KO dendritic cells with cytokine and nuclear-fractionation readouts","pmids":["40529355"],"confidence":"High","gaps":["Relationship between the canonical SKP1-Cullin1 and the PDLIM2-containing complex not reconciled","In vivo inflammatory phenotype of organismal Fbxo16 loss not characterized"]},{"year":null,"claim":"How FBXO16 selects among its multiple unrelated substrates (β-catenin, hnRNPL, p65, ULK1) and whether these activities operate in the same cells or are context-restricted remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of FBXO16 substrate-binding interface","No unifying recognition motif or post-translational trigger identified across substrates","Physiological (non-cancer) roles largely uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,4]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[2,4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2,4]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1,4]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,2,4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[4]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[3]}],"complexes":["SCF (SKP1-Cullin1-FBXO16) E3 ubiquitin ligase","PDLIM2-Cullin1-Skp1 ubiquitin ligase"],"partners":["SKP1","CUL1","CTNNB1","HNRNPL","RELA","ULK1","PDLIM2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8IX29","full_name":"F-box only protein 16","aliases":[],"length_aa":292,"mass_kda":34.6,"function":"Substrate recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Functions as a putative tumor suppressor by targeting nuclear beta-catenin/CTNNB1 for degradation independently of upstream activating signals, thereby inhibiting epithelial-to-mesenchymal transition (PubMed:30714168). Controls the ubiquitination and degradation of hnRNPL (PubMed:34333526). Negatively regulates NF-kappa-B signaling by mediating the polyubiquitination and degradation of RELA (PubMed:40529355). Inhibits autophagy by promoting 'Lys-48'-linked polyubiquitination of the serine/threonine-protein kinase ULK1 (PubMed:39384743)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q8IX29/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FBXO16","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FBXO16","total_profiled":1310},"omim":[{"mim_id":"608519","title":"F-BOX ONLY PROTEIN 16; FBXO16","url":"https://www.omim.org/entry/608519"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"},{"location":"Plasma membrane","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"epididymis","ntpm":17.3},{"tissue":"pituitary gland","ntpm":16.7}],"url":"https://www.proteinatlas.org/search/FBXO16"},"hgnc":{"alias_symbol":["FBX16"],"prev_symbol":[]},"alphafold":{"accession":"Q8IX29","domains":[{"cath_id":"-","chopping":"29-85","consensus_level":"high","plddt":92.7763,"start":29,"end":85},{"cath_id":"1.20.1280.50","chopping":"89-142_149-164","consensus_level":"high","plddt":94.4776,"start":89,"end":164}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IX29","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IX29-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IX29-F1-predicted_aligned_error_v6.png","plddt_mean":70.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FBXO16","jax_strain_url":"https://www.jax.org/strain/search?query=FBXO16"},"sequence":{"accession":"Q8IX29","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8IX29.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8IX29/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IX29"}},"corpus_meta":[{"pmid":"30530053","id":"PMC_30530053","title":"Attenuation of Tumor Suppressive Function of FBXO16 Ubiquitin Ligase Activates Wnt Signaling In Glioblastoma.","date":"2018","source":"Neoplasia (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/30530053","citation_count":30,"is_preprint":false},{"pmid":"34333526","id":"PMC_34333526","title":"FBXO16-mediated hnRNPL ubiquitination and degradation plays a tumor suppressor role in ovarian cancer.","date":"2021","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/34333526","citation_count":30,"is_preprint":false},{"pmid":"30714168","id":"PMC_30714168","title":"F-box protein FBXO16 functions as a tumor suppressor by attenuating nuclear β-catenin function.","date":"2019","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/30714168","citation_count":28,"is_preprint":false},{"pmid":"36656640","id":"PMC_36656640","title":"Effect of mechanical unloading on genome-wide DNA methylation profile of the failing human heart.","date":"2023","source":"JCI insight","url":"https://pubmed.ncbi.nlm.nih.gov/36656640","citation_count":25,"is_preprint":false},{"pmid":"32164368","id":"PMC_32164368","title":"Gene Polymorphisms in Boar Spermatozoa and Their Associations with Post-Thaw Semen Quality.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32164368","citation_count":25,"is_preprint":false},{"pmid":"40585174","id":"PMC_40585174","title":"FUS Mislocalization Rewires a Cortical Gene Network to Drive Cognitive and Behavioral Impairment in ALS.","date":"2025","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40585174","citation_count":4,"is_preprint":false},{"pmid":"12243353","id":"PMC_12243353","title":"cDNA cloning and expression analysis of a novel human F-box only protein.","date":"2002","source":"Molecules and cells","url":"https://pubmed.ncbi.nlm.nih.gov/12243353","citation_count":4,"is_preprint":false},{"pmid":"39384743","id":"PMC_39384743","title":"MIR937 amplification potentiates ovarian cancer progression by attenuating FBXO16 inhibition on ULK1-mediated autophagy.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/39384743","citation_count":3,"is_preprint":false},{"pmid":"40529355","id":"PMC_40529355","title":"Fbxo16 mediates degradation of NF-κB p65 subunit and inhibits inflammatory response in dendritic cells.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/40529355","citation_count":1,"is_preprint":false},{"pmid":"40206361","id":"PMC_40206361","title":"RNA Sequencing Identifies Novel Signaling Pathways and Potential Drug Target Genes Induced by FOSL1 in Glioma Progression and Stemness.","date":"2025","source":"Biologics : targets & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/40206361","citation_count":0,"is_preprint":false},{"pmid":"41990482","id":"PMC_41990482","title":"Genome-wide in silico identification and characterization of the F-box gene family in water buffalo (Bubalus bubalis).","date":"2026","source":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/41990482","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8056,"output_tokens":1769,"usd":0.025351,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8602,"output_tokens":2852,"usd":0.057155,"stage2_stop_reason":"end_turn"},"total_usd":0.082506,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"FBXO16, as a component of the SCF E3 ubiquitin ligase complex, interacts with β-catenin and mediates its proteasomal degradation in a GSK-3β-independent manner. Specifically, the C-terminal region of FBXO16 targets nuclear β-catenin for K-48 linked poly-ubiquitination, inhibiting TCF4/LEF1-dependent Wnt signaling in glioblastoma cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, nuclear fractionation, loss-of-function/gain-of-function experiments in GBM cells\",\n      \"journal\": \"Neoplasia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and ubiquitination assay with K48-linkage specificity, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"30530053\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FBXO16 forms an SCF (SKP1-Cullin1-FBXO16) complex that physically interacts with the C-terminal domain of β-catenin and promotes its K48-linked polyubiquitination and subsequent 26S proteasomal degradation. FBXO16 depletion increases nuclear β-catenin levels, promoting EMT, cell invasion, and tumor growth in breast cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, in vivo ubiquitination assay, siRNA knockdown with proliferation/invasion readouts, clinical breast cancer sample analysis\",\n      \"journal\": \"The Journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, ubiquitination assays, and KD phenotype with multiple readouts, single lab\",\n      \"pmids\": [\"30714168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"FBXO16 assembles a canonical SCF ubiquitin ligase complex via its F-box domain and constitutively targets hnRNPL for proteasomal degradation. FBXO16 interacts specifically with the RRM3 domain of hnRNPL through its C-terminal region, and loss of FBXO16 leads to hnRNPL accumulation that activates multiple oncogenic signaling pathways in ovarian cancer.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping pulldowns, siRNA knockdown and CRISPR depletion, ubiquitination assay, in vivo tumor growth assay, domain-deletion mutants\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP with domain mapping, in vivo ubiquitination, KO rescue experiments, in vitro and in vivo tumor models, multiple orthogonal methods in single lab\",\n      \"pmids\": [\"34333526\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FBXO16 negatively regulates ULK1 by targeting it for degradation; miR-937-5p (a product of MIR937 amplification) binds the 3' UTR of FBXO16 transcript to suppress FBXO16 expression, thereby relieving FBXO16-mediated degradation of ULK1 and enhancing autophagy and proliferation in high-grade serous ovarian cancer cells.\",\n      \"method\": \"miRNA target binding assay (3' UTR luciferase), siRNA/CRISPR deletion of MIR937, rescue assays, autophagy flux measurements, cell proliferation assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — 3' UTR binding validated, epistasis rescue confirmed, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"39384743\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Fbxo16 functions as a substrate-recognition receptor for the NF-κB p65 subunit within a PDLIM2-Cullin1-Skp1 ubiquitin ligase complex. Fbxo16 binds p65, promotes its polyubiquitination and proteasomal degradation, suppresses NF-κB transactivation, and Fbxo16 deficiency in dendritic cells results in increased nuclear p65 and enhanced proinflammatory cytokine production. Fbxo16 did not promote degradation of STAT3 or STAT4.\",\n      \"method\": \"siRNA screen of F-box proteins, Co-immunoprecipitation, ubiquitination assay, Fbxo16 KO dendritic cells with cytokine and nuclear fractionation readouts, STAT3/STAT4 functional assays (negative control)\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, in vivo ubiquitination, KO functional readout with multiple orthogonal methods, substrate specificity confirmed by negative controls for STAT3/STAT4\",\n      \"pmids\": [\"40529355\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"FBXO16 was identified as a novel human F-box protein encoded by a gene on chromosome 8p12, consisting of 9 exons spanning 67,816 bp of genomic DNA, with 90% amino acid identity to mouse Fbxo16. RT-PCR detected expression in heart, spleen, and colon.\",\n      \"method\": \"cDNA cloning from human fetal brain library, Northern blot, RT-PCR, genomic mapping\",\n      \"journal\": \"Molecules and cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — initial cloning and expression characterization, replicated by later functional studies confirming F-box protein identity\",\n      \"pmids\": [\"12243353\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FBXO16 is an F-box protein that functions as the substrate-recognition subunit of SCF (SKP1-Cullin1-FBXO16) E3 ubiquitin ligase complexes, targeting multiple substrates—including nuclear β-catenin, hnRNPL, NF-κB p65, and ULK1—for K48-linked polyubiquitination and 26S proteasomal degradation, thereby suppressing Wnt/β-catenin signaling, oncogenic RNA-binding protein activity, NF-κB-mediated inflammation, and autophagy in a context-dependent manner.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FBXO16 is an F-box protein that serves as the substrate-recognition subunit of SCF (SKP1–Cullin1–FBXO16) E3 ubiquitin ligase complexes, directing diverse substrates toward K48-linked polyubiquitination and 26S proteasomal degradation [#0, #2]. A recurrent theme across studies is its tumor-suppressive role through control of nuclear signaling pools: its C-terminal region binds nuclear β-catenin and drives its degradation in a GSK-3β-independent manner, restraining TCF4/LEF1-dependent Wnt signaling, with depletion promoting EMT, invasion, and tumor growth [#0, #1]. FBXO16 also constitutively targets the RNA-binding protein hnRNPL—via its RRM3 domain—for degradation, and its loss leads to hnRNPL accumulation and activation of oncogenic signaling in ovarian cancer [#2]. Beyond cancer signaling, FBXO16 acts as the substrate receptor that delivers the NF-κB p65 subunit for ubiquitination, suppressing NF-κB transactivation and proinflammatory cytokine production in dendritic cells, with substrate specificity confirmed by its failure to degrade STAT3 or STAT4 [#4]. It additionally limits autophagy by degrading ULK1; this brake is relieved when miR-937-5p represses FBXO16 expression [#3]. FBXO16 was originally identified as a human F-box gene on chromosome 8p12 [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Before any functional role was known, the question was whether FBXO16 was a bona fide F-box gene; cloning established it as a novel human F-box protein with a defined genomic structure and tissue expression.\",\n      \"evidence\": \"cDNA cloning from a human fetal brain library, Northern blot, RT-PCR, and genomic mapping to chromosome 8p12\",\n      \"pmids\": [\"12243353\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No substrate or biochemical activity assigned at this stage\", \"F-box partner subunits (SKP1/Cullin1) not yet demonstrated\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The first substrate question—what does FBXO16 ubiquitinate—was answered by showing it targets nuclear β-catenin for K48-linked degradation independently of GSK-3β, defining a tumor-suppressive node in Wnt signaling.\",\n      \"evidence\": \"Co-IP, K48-specific ubiquitination assays, and nuclear fractionation with loss/gain-of-function in glioblastoma cells\",\n      \"pmids\": [\"30530053\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of nuclear targeting/recruitment of FBXO16 to β-catenin unclear\", \"Single-lab finding in one tumor context\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extending the β-catenin model, this work confirmed assembly of the SKP1-Cullin1-FBXO16 SCF complex on β-catenin's C-terminal domain and linked its loss to EMT and metastatic phenotypes in breast cancer.\",\n      \"evidence\": \"Reciprocal Co-IP, in vivo ubiquitination assay, siRNA knockdown with invasion/proliferation readouts, and clinical sample analysis\",\n      \"pmids\": [\"30714168\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not resolve whether nuclear vs cytoplasmic β-catenin pools are differentially targeted\", \"Upstream regulation of FBXO16 abundance not addressed\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"The substrate repertoire was broadened beyond β-catenin by demonstrating that FBXO16 constitutively degrades the RNA-binding protein hnRNPL via its RRM3 domain, connecting the ligase to control of oncogenic RNA-processing activity.\",\n      \"evidence\": \"Reciprocal Co-IP with domain mapping, in vivo ubiquitination, CRISPR/siRNA depletion with KO rescue, and in vitro/in vivo ovarian tumor models\",\n      \"pmids\": [\"34333526\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream oncogenic pathways activated by hnRNPL not fully delineated\", \"Whether β-catenin and hnRNPL are degraded by the same cellular pool of FBXO16 unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"How FBXO16 itself is suppressed in cancer, and what this releases, was addressed by showing miR-937-5p represses FBXO16 to stabilize ULK1 and enhance autophagy—implicating FBXO16 as an autophagy brake.\",\n      \"evidence\": \"3' UTR luciferase binding assay, CRISPR deletion of MIR937, rescue and autophagy-flux measurements in high-grade serous ovarian cancer cells\",\n      \"pmids\": [\"39384743\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitination of ULK1 by an SCF-FBXO16 complex not biochemically mapped here\", \"Single-lab epistasis model\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A distinct immune role was established by identifying FBXO16 as the p65 substrate receptor within a PDLIM2-Cullin1-Skp1 ligase, with degradation specificity validated against STAT3/STAT4 negative controls, linking it to NF-κB-mediated inflammation.\",\n      \"evidence\": \"siRNA screen of F-box proteins, Co-IP, ubiquitination assay, and Fbxo16 KO dendritic cells with cytokine and nuclear-fractionation readouts\",\n      \"pmids\": [\"40529355\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relationship between the canonical SKP1-Cullin1 and the PDLIM2-containing complex not reconciled\", \"In vivo inflammatory phenotype of organismal Fbxo16 loss not characterized\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How FBXO16 selects among its multiple unrelated substrates (β-catenin, hnRNPL, p65, ULK1) and whether these activities operate in the same cells or are context-restricted remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of FBXO16 substrate-binding interface\", \"No unifying recognition motif or post-translational trigger identified across substrates\", \"Physiological (non-cancer) roles largely uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 4]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 2, 4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\n      \"SCF (SKP1-Cullin1-FBXO16) E3 ubiquitin ligase\",\n      \"PDLIM2-Cullin1-Skp1 ubiquitin ligase\"\n    ],\n    \"partners\": [\n      \"SKP1\",\n      \"CUL1\",\n      \"CTNNB1\",\n      \"HNRNPL\",\n      \"RELA\",\n      \"ULK1\",\n      \"PDLIM2\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}