{"gene":"FBXO28","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2016,"finding":"FBXO28 interacts and colocalizes with topoisomerase IIα throughout the cell cycle; depletion of FBXO28 increases topoisomerase IIα-dependent DNA decatenation activity, and blocking the FBXO28–topoisomerase IIα interaction causes multinucleated cells, indicating that FBXO28 regulates topoisomerase IIα decatenation activity and is required for proper mitotic progression (loss of function causes lagging chromosomes, multipolar spindles, and multinucleation).","method":"Co-immunoprecipitation, co-localization, siRNA knockdown, functional decatenation assay, live-cell imaging","journal":"Cell cycle (Georgetown, Tex.)","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP/co-localization plus functional decatenation assay plus loss-of-function phenotype, multiple orthogonal methods in a single focused study","pmids":["27754753"],"is_preprint":false},{"year":2019,"finding":"SCFFBXO28 is the E3 ligase responsible for its own self-ubiquitination and proteasomal degradation: deletion of the F-box domain stabilizes FBXO28, inhibition of the neddylation pathway (required for SCF activation) prolongs FBXO28 half-life, and knockdown of endogenous FBXO28 upregulates exogenous FBXO28, demonstrating auto-regulatory self-ubiquitination.","method":"Ubiquitination assay, cycloheximide chase, pharmacological neddylation inhibition (MLN4924), F-box domain deletion mutant, siRNA knockdown","journal":"Cellular signalling","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro ubiquitination assay combined with mutagenesis (F-box deletion), pharmacological and genetic inhibition, multiple orthogonal approaches in one study","pmids":["31678254"],"is_preprint":false},{"year":2019,"finding":"FBXO28 forms a protein complex with TRAF6 that binds ERK5 and enhances K63-linked ubiquitination and subsequent phosphorylation of ERK5, leading to MZF1 expression, MZF1-dependent RGC-32 upregulation, and glomerular mesangial cell proliferation in response to sublytic C5b-9 stimulation.","method":"Co-immunoprecipitation (protein complex identification), K63-ubiquitination assay, siRNA knockdown in vitro and in vivo (rat Thy-1 nephritis model), Western blot, promoter analysis","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus functional ubiquitination assay plus in vivo knockdown, single lab, multiple orthogonal methods","pmids":["31184423"],"is_preprint":false},{"year":2023,"finding":"FBXO28 directly binds SNAI2 and, as an SCF E3 ubiquitin ligase, targets SNAI2 for ubiquitin-proteasome degradation; PKA cooperates with FBXO28 in this process. Loss of FBXO28-mediated SNAI2 degradation promotes epithelial-mesenchymal transition and liver cancer metastasis.","method":"Co-immunoprecipitation, ubiquitination assay, in vitro and in vivo invasion/metastasis assays, Western blot, siRNA/overexpression","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus ubiquitination assay plus in vivo xenograft model, single lab, multiple orthogonal methods","pmids":["37596321"],"is_preprint":false},{"year":2022,"finding":"PFKFB4 interacts with FBXO28 (identified by mass spectrometry of immunoprecipitated PFKFB4); PFKFB4 regulates HIF-1α ubiquitylation and proteasomal degradation mediated by the ubiquitin ligase activity of FBXO28 in glioblastoma cells.","method":"Mass spectrometry of immunoprecipitated PFKFB4, Western blot (HIF-1α protein levels), siRNA silencing, ubiquitylation assay","journal":"Oncogenesis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-based interaction identification plus functional ubiquitylation readout, single lab, two orthogonal methods","pmids":["36115843"],"is_preprint":false},{"year":2023,"finding":"FBXO28 directly binds SMARCC2 (identified by immunoprecipitation–mass spectrometry) and promotes its ubiquitination and proteasomal degradation, thereby enhancing pancreatic cancer cell proliferation, invasion, and metastasis; overexpression of SMARCC2 reverses these pro-tumorigenic effects.","method":"Immunoprecipitation–mass spectrometry, ubiquitination assay, rescue (SMARCC2 overexpression), in vitro and in vivo functional assays","journal":"Aging","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-based substrate identification plus ubiquitination assay plus functional rescue, single lab","pmids":["37348029"],"is_preprint":false},{"year":2024,"finding":"FBXO28 directly binds RAB27A and promotes its K48-linked ubiquitinated degradation; upregulation of RAB27A reverses the FBXO28-mediated improvement in lipid metabolism and inflammation, establishing RAB27A as a bona fide substrate of FBXO28 in the context of hyperlipidemia.","method":"Co-immunoprecipitation, immunofluorescence, ubiquitination assay, cycloheximide chase, in vivo mouse (HFD) model, rescue (RAB27A overexpression)","journal":"Journal of endocrinological investigation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus ubiquitination assay plus in vivo model plus rescue experiment, single lab, multiple orthogonal methods","pmids":["38696123"],"is_preprint":false},{"year":2024,"finding":"Fbxo28 localizes to chromosomes and acentriolar microtubule-organizing centers (aMTOCs) in mouse oocytes; depletion of Fbxo28 causes defects in spindle morphology and spindle migration (without affecting polar body extrusion rate), disrupts cortical and cytoplasmic actin assembly, and reduces expression of ARPC2 and ARP3; these defects are rescued by exogenous Fbxo28 mRNA, establishing a role in actin-based asymmetric meiotic division.","method":"Morpholino oligonucleotide knockdown, mRNA rescue, immunofluorescence staining, timelapse confocal microscopy, chromosome spreading, Western blot","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — morpholino knockdown with mRNA rescue plus live imaging plus immunofluorescence, single lab, multiple orthogonal methods","pmids":["38960234"],"is_preprint":false},{"year":2018,"finding":"FBXO28, as the substrate-recruiting component of the SCF ligase complex, regulates pancreatic β-cell survival; genetic silencing of FBXO28 impairs β-cell survival under diabetogenic conditions, and restoration of FBXO28 protects β-cells from apoptosis, without affecting insulin content or glucose-stimulated insulin secretion.","method":"siRNA knockdown, overexpression, cell viability/apoptosis assays, glucose-stimulated insulin secretion assay in human islets","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — loss-of-function and gain-of-function with defined survival phenotype, single lab, limited mechanistic depth on downstream substrate","pmids":["29587369"],"is_preprint":false},{"year":2020,"finding":"miR-184 directly targets FBXO28 (validated by luciferase reporter assay); inhibition of miR-184 increases FBXO28 expression and reduces oxidative stress, inflammation, and apoptosis in H2O2-treated cardiomyocytes, placing FBXO28 downstream of miR-184 in this pathway.","method":"Luciferase reporter assay (direct targeting validation), miR-184 inhibitor transfection, Western blot, TUNEL assay, MTT assay","journal":"European review for medical and pharmacological sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — luciferase reporter confirms targeting but mechanistic detail of how FBXO28 mediates protection is not established; single lab, single method for the interaction","pmids":["33215444"],"is_preprint":false},{"year":2026,"finding":"FBXO28 is recruited by APLNR (apelin receptor) upon A13 ligand stimulation and promotes K48-linked ubiquitination and proteasomal degradation of Rab27a; APLNR knockdown or proteasome inhibition (MG132) abrogates this effect, and A13 enhances FBXO28–Rab27a complex formation in an APLNR-dependent manner.","method":"Co-immunoprecipitation (FBXO28–Rab27a complex), K48-ubiquitination assay, APLNR knockdown, MG132 proteasome inhibition, in vivo murine allergy model","journal":"Immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus ubiquitination assay plus genetic knockdown plus pharmacological inhibition, single lab, multiple orthogonal methods","pmids":["42068044"],"is_preprint":false}],"current_model":"FBXO28 is an F-box protein that functions as the substrate-recognition subunit of SCF (SKP1/CUL1/F-box) E3 ubiquitin ligase complexes, directly ubiquitinating and targeting multiple substrates—including SNAI2, SMARCC2, RAB27A, HIF-1α (in cooperation with PFKFB4), and ERK5 (via a complex with TRAF6)—for proteasomal degradation, while also regulating topoisomerase IIα decatenation activity and actin-based spindle migration during meiosis; additionally, FBXO28 undergoes SCF-mediated auto-ubiquitination for its own degradation, and pathogenic loss-of-function variants cause developmental and epileptic encephalopathy."},"narrative":{"mechanistic_narrative":"FBXO28 is an F-box protein that serves as the substrate-recognition subunit of SCF (SKP1/CUL1/F-box) E3 ubiquitin ligase complexes, directing ubiquitination of diverse substrates for proteasomal degradation across processes spanning cell division, oncogenesis, and metabolism [PMID:31678254, PMID:37596321]. As an SCF component it directly binds and ubiquitinates multiple targets, including the EMT regulator SNAI2 in cooperation with PKA [PMID:37596321], the chromatin-remodeling factor SMARCC2 in pancreatic cancer [PMID:37348029], and the small GTPase RAB27A via K48-linked chains [PMID:38696123]; it also assembles a complex with TRAF6 that promotes K63-linked ubiquitination and activation of ERK5 [PMID:31184423], and supports PFKFB4-dependent ubiquitylation of HIF-1α [PMID:36115843]. SCFᶠᴮˣᵒ²⁸ activity additionally drives FBXO28 auto-ubiquitination and self-degradation, a neddylation-dependent autoregulatory loop [PMID:31678254]. Beyond its ligase function, FBXO28 interacts with topoisomerase IIα to restrain its decatenation activity and ensure proper mitotic chromosome segregation, with loss of function producing lagging chromosomes, multipolar spindles, and multinucleation [PMID:27754753], and it localizes to chromosomes and acentriolar MTOCs in oocytes where it governs actin-based spindle migration during asymmetric meiotic division [PMID:38960234].","teleology":[{"year":2016,"claim":"Established the first defined cellular role for FBXO28 by showing it physically restrains topoisomerase IIα decatenation activity to safeguard mitotic fidelity, rather than acting purely as a degradation adaptor.","evidence":"Reciprocal co-IP, co-localization, siRNA knockdown, decatenation assay, and live-cell imaging in human cells","pmids":["27754753"],"confidence":"High","gaps":["Whether topoisomerase IIα regulation requires SCF ligase activity or is a non-degradative interaction is not resolved","No structural basis for the FBXO28–TOP2A interface"]},{"year":2018,"claim":"Linked FBXO28 as an SCF substrate-recruiting subunit to pancreatic β-cell survival, extending its relevance to metabolic/endocrine biology.","evidence":"siRNA knockdown, overexpression, and apoptosis/insulin-secretion assays in human islets","pmids":["29587369"],"confidence":"Medium","gaps":["The degradation substrate mediating the survival effect was not identified","Mechanism downstream of FBXO28 in β-cells unknown"]},{"year":2019,"claim":"Defined FBXO28's autoregulation, showing SCFᶠᴮˣᵒ²⁸ self-ubiquitinates in a neddylation- and F-box-dependent manner, establishing its own turnover control.","evidence":"Ubiquitination assay, cycloheximide chase, MLN4924 inhibition, F-box deletion mutant, siRNA in human cells","pmids":["31678254"],"confidence":"High","gaps":["Physiological signals controlling auto-degradation not defined","Lysine residues mediating self-ubiquitination not mapped"]},{"year":2019,"claim":"Showed FBXO28 also participates in non-degradative K63-linked ubiquitination by forming a complex with TRAF6 to activate ERK5 signaling, broadening its ubiquitin chain repertoire.","evidence":"Co-IP, K63-ubiquitination assay, in vitro and in vivo (rat Thy-1 nephritis) knockdown, promoter analysis","pmids":["31184423"],"confidence":"Medium","gaps":["Whether FBXO28 functions here within canonical SCF is unclear","Direct E3 versus scaffolding role with TRAF6 not dissected"]},{"year":2022,"claim":"Implicated FBXO28 in hypoxia signaling, showing PFKFB4 directs FBXO28 ligase activity toward HIF-1α ubiquitylation and degradation in glioblastoma.","evidence":"Mass spectrometry of immunoprecipitated PFKFB4, ubiquitylation assay, siRNA, Western blot","pmids":["36115843"],"confidence":"Medium","gaps":["Direct binding of FBXO28 to HIF-1α not demonstrated","How PFKFB4 redirects substrate selection unknown"]},{"year":2023,"claim":"Identified SNAI2 and SMARCC2 as direct degradation substrates, framing FBXO28 as a tumor suppressor restraining EMT and tumor progression.","evidence":"Co-IP/IP-MS, ubiquitination assays, rescue and in vitro/in vivo metastasis assays in liver and pancreatic cancer models","pmids":["37596321","37348029"],"confidence":"Medium","gaps":["Degron motifs in substrates not mapped","Context determining substrate choice across tissues unresolved"]},{"year":2024,"claim":"Established RAB27A as a K48-linked degradation substrate and defined a meiotic role, showing FBXO28 controls actin assembly and asymmetric spindle migration in oocytes.","evidence":"Co-IP, ubiquitination, CHX chase, in vivo HFD model and rescue (RAB27A); morpholino knockdown with mRNA rescue, live imaging, IF in mouse oocytes","pmids":["38696123","38960234"],"confidence":"Medium","gaps":["Whether oocyte actin defects depend on RAB27A degradation is untested","Link between FBXO28 and ARPC2/ARP3 expression is indirect"]},{"year":2026,"claim":"Placed FBXO28-mediated RAB27A degradation downstream of receptor signaling, showing APLNR recruits FBXO28 upon ligand stimulation to drive K48-linked Rab27a turnover.","evidence":"Co-IP, K48-ubiquitination assay, APLNR knockdown, MG132 inhibition, in vivo murine allergy model","pmids":["42068044"],"confidence":"Medium","gaps":["Mechanism of APLNR-dependent FBXO28 recruitment not defined","Whether this represents the same SCF complex active elsewhere is unclear"]},{"year":null,"claim":"How FBXO28 selects among its many substrates in a tissue- and signal-specific manner, and whether its degradative and non-degradative (K63, topoisomerase-regulatory) activities share a common SCF assembly, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of FBXO28 substrate-binding interface","Substrate degrons and recruitment cofactors largely unmapped","Relationship between mitotic, meiotic, and ligase functions undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[1,3,5,6]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,2,3,5,6,10]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[10]}],"localization":[{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[0,7]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,3,5,6]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,7]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,4,10]}],"complexes":["SCF (SKP1/CUL1/F-box) E3 ubiquitin ligase","FBXO28-TRAF6 complex"],"partners":["TOP2A","TRAF6","SNAI2","SMARCC2","RAB27A","PFKFB4","APLNR","ERK5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NVF7","full_name":"F-box only protein 28","aliases":[],"length_aa":368,"mass_kda":41.1,"function":"Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex, promoting ubiquitination and proteasomal degradation of specific target proteins including TOP2A, RAB27A or itself (PubMed:27754753, PubMed:31678254). Regulates topoisomerase IIalpha/TOP2A decatenation activity and plays an important role in maintaining genomic stability (PubMed:27754753). Plays a role in lipid metabolism and inflammation through the ubiquitinated degradation of RAB27A (By similarity). Strongly regulates beta-cell survival without having any significant independent effect on insulin secretion (PubMed:29587369). Plays an essential role in spindle morphology and actin-based spindle migration probably through the ARPC2/ARP3 signaling pathway (By similarity)","subcellular_location":"Chromosome, centromere, kinetochore; Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q9NVF7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FBXO28","classification":"Not Classified","n_dependent_lines":91,"n_total_lines":1208,"dependency_fraction":0.07533112582781457},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CKAP4","stoichiometry":0.2},{"gene":"H1F0","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"HMGN5","stoichiometry":0.2},{"gene":"NUMA1","stoichiometry":0.2},{"gene":"PAK2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/FBXO28","total_profiled":1310},"omim":[{"mim_id":"619777","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 100; DEE100","url":"https://www.omim.org/entry/619777"},{"mim_id":"612530","title":"CHROMOSOME 1q41-q42 DELETION SYNDROME","url":"https://www.omim.org/entry/612530"},{"mim_id":"609100","title":"F-BOX ONLY PROTEIN 28; FBXO28","url":"https://www.omim.org/entry/609100"},{"mim_id":"308350","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 1; DEE1","url":"https://www.omim.org/entry/308350"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Focal adhesion sites","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FBXO28"},"hgnc":{"alias_symbol":["FLJ10766","KIAA0483","Fbx28","CENP-30"],"prev_symbol":[]},"alphafold":{"accession":"Q9NVF7","domains":[{"cath_id":"-","chopping":"67-222","consensus_level":"high","plddt":93.666,"start":67,"end":222}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NVF7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NVF7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NVF7-F1-predicted_aligned_error_v6.png","plddt_mean":76.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FBXO28","jax_strain_url":"https://www.jax.org/strain/search?query=FBXO28"},"sequence":{"accession":"Q9NVF7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NVF7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NVF7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NVF7"}},"corpus_meta":[{"pmid":"24357076","id":"PMC_24357076","title":"Refinement of the critical region of 1q41q42 microdeletion syndrome identifies FBXO28 as a candidate causative gene for intellectual disability and seizures.","date":"2013","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/24357076","citation_count":25,"is_preprint":false},{"pmid":"37596321","id":"PMC_37596321","title":"FBXO28 suppresses liver cancer invasion and metastasis by promoting PKA-dependent SNAI2 degradation.","date":"2023","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/37596321","citation_count":21,"is_preprint":false},{"pmid":"33215444","id":"PMC_33215444","title":"Inhibition of microRNA-184 reduces H2O2-mediated cardiomyocyte injury via targeting FBXO28.","date":"2020","source":"European review for medical and pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33215444","citation_count":19,"is_preprint":false},{"pmid":"31184423","id":"PMC_31184423","title":"Sublytic C5b-9 induces proliferation of glomerular mesangial cells via ERK5/MZF1/RGC-32 axis activated by FBXO28-TRAF6 complex.","date":"2019","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31184423","citation_count":15,"is_preprint":false},{"pmid":"31678254","id":"PMC_31678254","title":"SCFFBXO28-mediated self-ubiquitination of FBXO28 promotes its degradation.","date":"2019","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/31678254","citation_count":14,"is_preprint":false},{"pmid":"29587369","id":"PMC_29587369","title":"An SCFFBXO28 E3 Ligase Protects Pancreatic β-Cells from Apoptosis.","date":"2018","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/29587369","citation_count":14,"is_preprint":false},{"pmid":"27754753","id":"PMC_27754753","title":"Fbxo28 promotes mitotic progression and regulates topoisomerase IIα-dependent DNA decatenation.","date":"2016","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/27754753","citation_count":13,"is_preprint":false},{"pmid":"33280099","id":"PMC_33280099","title":"FBXO28 causes developmental and epileptic encephalopathy with profound intellectual disability.","date":"2020","source":"Epilepsia","url":"https://pubmed.ncbi.nlm.nih.gov/33280099","citation_count":13,"is_preprint":false},{"pmid":"36115843","id":"PMC_36115843","title":"PFKFB4 interacts with FBXO28 to promote HIF-1α signaling in glioblastoma.","date":"2022","source":"Oncogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/36115843","citation_count":13,"is_preprint":false},{"pmid":"30160831","id":"PMC_30160831","title":"A novel FBXO28 frameshift mutation in a child with developmental delay, dysmorphic features, and intractable epilepsy: A second gene that may contribute to the 1q41-q42 deletion phenotype.","date":"2018","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/30160831","citation_count":11,"is_preprint":false},{"pmid":"38267923","id":"PMC_38267923","title":"FBXO28 promotes cell proliferation, migration and invasion via upregulation of the TGF-beta1/SMAD2/3 signaling pathway in ovarian cancer.","date":"2024","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/38267923","citation_count":9,"is_preprint":false},{"pmid":"28179588","id":"PMC_28179588","title":"TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/28179588","citation_count":9,"is_preprint":false},{"pmid":"37348029","id":"PMC_37348029","title":"FBXO28 promotes proliferation, invasion, and metastasis of pancreatic cancer cells through regulation of SMARCC2 ubiquitination.","date":"2023","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/37348029","citation_count":7,"is_preprint":false},{"pmid":"38696123","id":"PMC_38696123","title":"FBXO28 reduces high-fat diet-induced hyperlipidemia in mice by alleviating abnormal lipid metabolism and inflammatory responses.","date":"2024","source":"Journal of endocrinological investigation","url":"https://pubmed.ncbi.nlm.nih.gov/38696123","citation_count":6,"is_preprint":false},{"pmid":"38960234","id":"PMC_38960234","title":"Fbxo28 is essential for spindle migration and morphology during mouse oocyte meiosis I.","date":"2024","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/38960234","citation_count":1,"is_preprint":false},{"pmid":"39432981","id":"PMC_39432981","title":"Acetazolamide as a therapeutic alternative for central sleep apnea in pediatric patient with FBXO28 gene mutation: A case report and review of literature.","date":"2024","source":"Sleep medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39432981","citation_count":1,"is_preprint":false},{"pmid":"37543484","id":"PMC_37543484","title":"Neurochemistry evaluated by magnetic resonance spectroscopy in a patient with FBXO28-related developmental and epileptic encephalopathy.","date":"2023","source":"Brain & development","url":"https://pubmed.ncbi.nlm.nih.gov/37543484","citation_count":1,"is_preprint":false},{"pmid":"37761828","id":"PMC_37761828","title":"3' UTR Deletion of FBXO28 in a Patient with Brain Abnormalities and Developmental Delay.","date":"2023","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/37761828","citation_count":0,"is_preprint":false},{"pmid":"41470009","id":"PMC_41470009","title":"Upregulation of miR-502-5p in traumatic spinal cord injury modulates neuroinflammation and oxidative stress by targeting FBXO28.","date":"2025","source":"Journal of orthopaedic surgery and research","url":"https://pubmed.ncbi.nlm.nih.gov/41470009","citation_count":0,"is_preprint":false},{"pmid":"42068044","id":"PMC_42068044","title":"Novel Pathway for Intercepting Granular Exocytosis: A13 Engages APLNR to Drive FBXO28-Mediated Ubiquitination and Proteasomal Clearance of Rab27a in Allergic Inflammation.","date":"2026","source":"Immunology","url":"https://pubmed.ncbi.nlm.nih.gov/42068044","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.12.659252","title":"Nanopore Sequencing Unveils Somatic Structural Variations as Biomarkers in Laryngeal squamous cell carcinoma Genomes","date":"2025-06-17","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.12.659252","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13087,"output_tokens":3033,"usd":0.042378,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10410,"output_tokens":3188,"usd":0.065875,"stage2_stop_reason":"end_turn"},"total_usd":0.108253,"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\": 2016,\n      \"finding\": \"FBXO28 interacts and colocalizes with topoisomerase IIα throughout the cell cycle; depletion of FBXO28 increases topoisomerase IIα-dependent DNA decatenation activity, and blocking the FBXO28–topoisomerase IIα interaction causes multinucleated cells, indicating that FBXO28 regulates topoisomerase IIα decatenation activity and is required for proper mitotic progression (loss of function causes lagging chromosomes, multipolar spindles, and multinucleation).\",\n      \"method\": \"Co-immunoprecipitation, co-localization, siRNA knockdown, functional decatenation assay, live-cell imaging\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP/co-localization plus functional decatenation assay plus loss-of-function phenotype, multiple orthogonal methods in a single focused study\",\n      \"pmids\": [\"27754753\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SCFFBXO28 is the E3 ligase responsible for its own self-ubiquitination and proteasomal degradation: deletion of the F-box domain stabilizes FBXO28, inhibition of the neddylation pathway (required for SCF activation) prolongs FBXO28 half-life, and knockdown of endogenous FBXO28 upregulates exogenous FBXO28, demonstrating auto-regulatory self-ubiquitination.\",\n      \"method\": \"Ubiquitination assay, cycloheximide chase, pharmacological neddylation inhibition (MLN4924), F-box domain deletion mutant, siRNA knockdown\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro ubiquitination assay combined with mutagenesis (F-box deletion), pharmacological and genetic inhibition, multiple orthogonal approaches in one study\",\n      \"pmids\": [\"31678254\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FBXO28 forms a protein complex with TRAF6 that binds ERK5 and enhances K63-linked ubiquitination and subsequent phosphorylation of ERK5, leading to MZF1 expression, MZF1-dependent RGC-32 upregulation, and glomerular mesangial cell proliferation in response to sublytic C5b-9 stimulation.\",\n      \"method\": \"Co-immunoprecipitation (protein complex identification), K63-ubiquitination assay, siRNA knockdown in vitro and in vivo (rat Thy-1 nephritis model), Western blot, promoter analysis\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus functional ubiquitination assay plus in vivo knockdown, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"31184423\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FBXO28 directly binds SNAI2 and, as an SCF E3 ubiquitin ligase, targets SNAI2 for ubiquitin-proteasome degradation; PKA cooperates with FBXO28 in this process. Loss of FBXO28-mediated SNAI2 degradation promotes epithelial-mesenchymal transition and liver cancer metastasis.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, in vitro and in vivo invasion/metastasis assays, Western blot, siRNA/overexpression\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus ubiquitination assay plus in vivo xenograft model, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"37596321\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PFKFB4 interacts with FBXO28 (identified by mass spectrometry of immunoprecipitated PFKFB4); PFKFB4 regulates HIF-1α ubiquitylation and proteasomal degradation mediated by the ubiquitin ligase activity of FBXO28 in glioblastoma cells.\",\n      \"method\": \"Mass spectrometry of immunoprecipitated PFKFB4, Western blot (HIF-1α protein levels), siRNA silencing, ubiquitylation assay\",\n      \"journal\": \"Oncogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-based interaction identification plus functional ubiquitylation readout, single lab, two orthogonal methods\",\n      \"pmids\": [\"36115843\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FBXO28 directly binds SMARCC2 (identified by immunoprecipitation–mass spectrometry) and promotes its ubiquitination and proteasomal degradation, thereby enhancing pancreatic cancer cell proliferation, invasion, and metastasis; overexpression of SMARCC2 reverses these pro-tumorigenic effects.\",\n      \"method\": \"Immunoprecipitation–mass spectrometry, ubiquitination assay, rescue (SMARCC2 overexpression), in vitro and in vivo functional assays\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-based substrate identification plus ubiquitination assay plus functional rescue, single lab\",\n      \"pmids\": [\"37348029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FBXO28 directly binds RAB27A and promotes its K48-linked ubiquitinated degradation; upregulation of RAB27A reverses the FBXO28-mediated improvement in lipid metabolism and inflammation, establishing RAB27A as a bona fide substrate of FBXO28 in the context of hyperlipidemia.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, ubiquitination assay, cycloheximide chase, in vivo mouse (HFD) model, rescue (RAB27A overexpression)\",\n      \"journal\": \"Journal of endocrinological investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus ubiquitination assay plus in vivo model plus rescue experiment, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"38696123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Fbxo28 localizes to chromosomes and acentriolar microtubule-organizing centers (aMTOCs) in mouse oocytes; depletion of Fbxo28 causes defects in spindle morphology and spindle migration (without affecting polar body extrusion rate), disrupts cortical and cytoplasmic actin assembly, and reduces expression of ARPC2 and ARP3; these defects are rescued by exogenous Fbxo28 mRNA, establishing a role in actin-based asymmetric meiotic division.\",\n      \"method\": \"Morpholino oligonucleotide knockdown, mRNA rescue, immunofluorescence staining, timelapse confocal microscopy, chromosome spreading, Western blot\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — morpholino knockdown with mRNA rescue plus live imaging plus immunofluorescence, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"38960234\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"FBXO28, as the substrate-recruiting component of the SCF ligase complex, regulates pancreatic β-cell survival; genetic silencing of FBXO28 impairs β-cell survival under diabetogenic conditions, and restoration of FBXO28 protects β-cells from apoptosis, without affecting insulin content or glucose-stimulated insulin secretion.\",\n      \"method\": \"siRNA knockdown, overexpression, cell viability/apoptosis assays, glucose-stimulated insulin secretion assay in human islets\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — loss-of-function and gain-of-function with defined survival phenotype, single lab, limited mechanistic depth on downstream substrate\",\n      \"pmids\": [\"29587369\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"miR-184 directly targets FBXO28 (validated by luciferase reporter assay); inhibition of miR-184 increases FBXO28 expression and reduces oxidative stress, inflammation, and apoptosis in H2O2-treated cardiomyocytes, placing FBXO28 downstream of miR-184 in this pathway.\",\n      \"method\": \"Luciferase reporter assay (direct targeting validation), miR-184 inhibitor transfection, Western blot, TUNEL assay, MTT assay\",\n      \"journal\": \"European review for medical and pharmacological sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — luciferase reporter confirms targeting but mechanistic detail of how FBXO28 mediates protection is not established; single lab, single method for the interaction\",\n      \"pmids\": [\"33215444\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"FBXO28 is recruited by APLNR (apelin receptor) upon A13 ligand stimulation and promotes K48-linked ubiquitination and proteasomal degradation of Rab27a; APLNR knockdown or proteasome inhibition (MG132) abrogates this effect, and A13 enhances FBXO28–Rab27a complex formation in an APLNR-dependent manner.\",\n      \"method\": \"Co-immunoprecipitation (FBXO28–Rab27a complex), K48-ubiquitination assay, APLNR knockdown, MG132 proteasome inhibition, in vivo murine allergy model\",\n      \"journal\": \"Immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus ubiquitination assay plus genetic knockdown plus pharmacological inhibition, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"42068044\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FBXO28 is an F-box protein that functions as the substrate-recognition subunit of SCF (SKP1/CUL1/F-box) E3 ubiquitin ligase complexes, directly ubiquitinating and targeting multiple substrates—including SNAI2, SMARCC2, RAB27A, HIF-1α (in cooperation with PFKFB4), and ERK5 (via a complex with TRAF6)—for proteasomal degradation, while also regulating topoisomerase IIα decatenation activity and actin-based spindle migration during meiosis; additionally, FBXO28 undergoes SCF-mediated auto-ubiquitination for its own degradation, and pathogenic loss-of-function variants cause developmental and epileptic encephalopathy.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"FBXO28 is an F-box protein that serves as the substrate-recognition subunit of SCF (SKP1/CUL1/F-box) E3 ubiquitin ligase complexes, directing ubiquitination of diverse substrates for proteasomal degradation across processes spanning cell division, oncogenesis, and metabolism [#1, #3]. As an SCF component it directly binds and ubiquitinates multiple targets, including the EMT regulator SNAI2 in cooperation with PKA [#3], the chromatin-remodeling factor SMARCC2 in pancreatic cancer [#5], and the small GTPase RAB27A via K48-linked chains [#6]; it also assembles a complex with TRAF6 that promotes K63-linked ubiquitination and activation of ERK5 [#2], and supports PFKFB4-dependent ubiquitylation of HIF-1\\u03b1 [#4]. SCF\\u1da0\\u1d2e\\u02e3\\u1d52\\u00b2\\u2078 activity additionally drives FBXO28 auto-ubiquitination and self-degradation, a neddylation-dependent autoregulatory loop [#1]. Beyond its ligase function, FBXO28 interacts with topoisomerase II\\u03b1 to restrain its decatenation activity and ensure proper mitotic chromosome segregation, with loss of function producing lagging chromosomes, multipolar spindles, and multinucleation [#0], and it localizes to chromosomes and acentriolar MTOCs in oocytes where it governs actin-based spindle migration during asymmetric meiotic division [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established the first defined cellular role for FBXO28 by showing it physically restrains topoisomerase II\\u03b1 decatenation activity to safeguard mitotic fidelity, rather than acting purely as a degradation adaptor.\",\n      \"evidence\": \"Reciprocal co-IP, co-localization, siRNA knockdown, decatenation assay, and live-cell imaging in human cells\",\n      \"pmids\": [\"27754753\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether topoisomerase II\\u03b1 regulation requires SCF ligase activity or is a non-degradative interaction is not resolved\", \"No structural basis for the FBXO28\\u2013TOP2A interface\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Linked FBXO28 as an SCF substrate-recruiting subunit to pancreatic \\u03b2-cell survival, extending its relevance to metabolic/endocrine biology.\",\n      \"evidence\": \"siRNA knockdown, overexpression, and apoptosis/insulin-secretion assays in human islets\",\n      \"pmids\": [\"29587369\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The degradation substrate mediating the survival effect was not identified\", \"Mechanism downstream of FBXO28 in \\u03b2-cells unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined FBXO28's autoregulation, showing SCF\\u1da0\\u1d2e\\u02e3\\u1d52\\u00b2\\u2078 self-ubiquitinates in a neddylation- and F-box-dependent manner, establishing its own turnover control.\",\n      \"evidence\": \"Ubiquitination assay, cycloheximide chase, MLN4924 inhibition, F-box deletion mutant, siRNA in human cells\",\n      \"pmids\": [\"31678254\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological signals controlling auto-degradation not defined\", \"Lysine residues mediating self-ubiquitination not mapped\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed FBXO28 also participates in non-degradative K63-linked ubiquitination by forming a complex with TRAF6 to activate ERK5 signaling, broadening its ubiquitin chain repertoire.\",\n      \"evidence\": \"Co-IP, K63-ubiquitination assay, in vitro and in vivo (rat Thy-1 nephritis) knockdown, promoter analysis\",\n      \"pmids\": [\"31184423\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether FBXO28 functions here within canonical SCF is unclear\", \"Direct E3 versus scaffolding role with TRAF6 not dissected\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated FBXO28 in hypoxia signaling, showing PFKFB4 directs FBXO28 ligase activity toward HIF-1\\u03b1 ubiquitylation and degradation in glioblastoma.\",\n      \"evidence\": \"Mass spectrometry of immunoprecipitated PFKFB4, ubiquitylation assay, siRNA, Western blot\",\n      \"pmids\": [\"36115843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding of FBXO28 to HIF-1\\u03b1 not demonstrated\", \"How PFKFB4 redirects substrate selection unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified SNAI2 and SMARCC2 as direct degradation substrates, framing FBXO28 as a tumor suppressor restraining EMT and tumor progression.\",\n      \"evidence\": \"Co-IP/IP-MS, ubiquitination assays, rescue and in vitro/in vivo metastasis assays in liver and pancreatic cancer models\",\n      \"pmids\": [\"37596321\", \"37348029\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Degron motifs in substrates not mapped\", \"Context determining substrate choice across tissues unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established RAB27A as a K48-linked degradation substrate and defined a meiotic role, showing FBXO28 controls actin assembly and asymmetric spindle migration in oocytes.\",\n      \"evidence\": \"Co-IP, ubiquitination, CHX chase, in vivo HFD model and rescue (RAB27A); morpholino knockdown with mRNA rescue, live imaging, IF in mouse oocytes\",\n      \"pmids\": [\"38696123\", \"38960234\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether oocyte actin defects depend on RAB27A degradation is untested\", \"Link between FBXO28 and ARPC2/ARP3 expression is indirect\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Placed FBXO28-mediated RAB27A degradation downstream of receptor signaling, showing APLNR recruits FBXO28 upon ligand stimulation to drive K48-linked Rab27a turnover.\",\n      \"evidence\": \"Co-IP, K48-ubiquitination assay, APLNR knockdown, MG132 inhibition, in vivo murine allergy model\",\n      \"pmids\": [\"42068044\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of APLNR-dependent FBXO28 recruitment not defined\", \"Whether this represents the same SCF complex active elsewhere is unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How FBXO28 selects among its many substrates in a tissue- and signal-specific manner, and whether its degradative and non-degradative (K63, topoisomerase-regulatory) activities share a common SCF assembly, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of FBXO28 substrate-binding interface\", \"Substrate degrons and recruitment cofactors largely unmapped\", \"Relationship between mitotic, meiotic, and ligase functions undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [1, 3, 5, 6]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 2, 3, 5, 6, 10]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 3, 5, 6]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 4, 10]}\n    ],\n    \"complexes\": [\"SCF (SKP1/CUL1/F-box) E3 ubiquitin ligase\", \"FBXO28-TRAF6 complex\"],\n    \"partners\": [\"TOP2A\", \"TRAF6\", \"SNAI2\", \"SMARCC2\", \"RAB27A\", \"PFKFB4\", \"APLNR\", \"ERK5\"],\n    \"other_free_text\": []\n  }\n}\n```","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}