{"gene":"FBXO25","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2005,"finding":"FBXO25 (hFBX25) was established as an F-box protein that interacts with Skp1 and Cul1, forming part of an SCF-type ubiquitin ligase complex. An atypical serine residue in the F-box domain was identified as crucial for hFBX25-Skp1 binding. FBXO25 localizes to the nucleus and is strongly expressed in brain tissue.","method":"Interaction verified by co-immunoprecipitation; F-box domain mutagenesis (serine residue); subcellular localization by immunochemistry; tissue expression by RT-PCR/immunoblot","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with mutagenesis in a single focused study, two orthogonal methods","pmids":["16278047"],"is_preprint":false},{"year":2006,"finding":"FBXO25 contains a functional F-box domain that binds Skp1 and thereby assembles with Roc1 and Cul1 into a productive SCF complex with ubiquitin ligase activity in vitro. FBXO25 is expressed in brain, kidney, and intestine but not striated muscle, and is not induced in atrophying muscle unlike its paralog atrogin-1.","method":"Co-immunoprecipitation; in vitro ubiquitin ligase activity assay; RT-PCR tissue expression; mouse fasting, dexamethasone, and streptozotocin-diabetes models","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — in vitro ligase assay plus co-IP, single lab, two orthogonal methods","pmids":["16714087"],"is_preprint":false},{"year":2008,"finding":"Endogenous FBXO25 accumulates in novel dot-like subnuclear structures (FBXO25-associated nuclear domains, FAND) that are distinct from clastosomes and contain ubiquitin conjugates, 20S proteasome, and Skp1. FAND are dynamic and disrupted by transcription inhibition (actinomycin D) or heat shock. FBXO25-dependent ubiquitin ligase activity in the nucleus prevents aggregation of polyglutamine-containing huntingtin in HEK293 cells.","method":"Confocal immunofluorescence with affinity-purified antibodies; biochemical fractionation; actinomycin D/heat-shock perturbation; huntingtin aggregation assay in HEK293 cells","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiments with functional consequence, single lab, multiple orthogonal methods","pmids":["18287534"],"is_preprint":false},{"year":2010,"finding":"Integrated proteomics (two-step affinity purification + MS and two-hybrid screen) identified 132 potential FBXO25-interacting partners. Beta-actin physically interacts via its N-terminus with FBXO25 and is enriched in FAND; inhibitors of actin polymerization disrupt FAND, indicating nuclear actin organization regulates these compartments. FBXO25 antibodies interfered with RNA polymerase II transcription in vitro.","method":"Two-step affinity purification followed by MS; two-hybrid screen; co-immunoprecipitation (beta-actin); actin polymerization inhibitors; in vitro RNA Pol II transcription assay with antibody interference","journal":"Proteomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal MS interactome plus functional in vitro assay, single lab","pmids":["20473970"],"is_preprint":false},{"year":2011,"finding":"Fbxo25 acts as an E3 ubiquitin ligase for cardiac transcription factors: it directly ubiquitinates Nkx2-5, Isl1, and Hand1, and facilitates proteasome-dependent degradation of Nkx2-5, Isl1, Hand1, and Mef2C. Fbxo25 is expressed in cardiomyocyte nuclei with higher levels in fetal versus adult heart, and its expression increases during ESC-derived cardiomyocyte development.","method":"Ubiquitination assays; proteasome inhibitor (MG132) rescue; immunofluorescence localization; immunoblot in cardiomyocytes and ESC differentiation model","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination assay plus degradation rescue, single lab, two methods","pmids":["21596019"],"is_preprint":false},{"year":2013,"finding":"FBXO25 interacts with and mediates ubiquitination and proteasomal degradation of ELK-1 in HEK293T cells, functioning as the substrate-recognition subunit of SCF(FBXO25). FBXO25 overexpression suppresses induction of ELK-1 target genes c-fos and egr-1 in response to phorbol ester.","method":"Human protein microarray ubiquitination screen; co-immunoprecipitation; ubiquitination assay; cycloheximide chase; gene expression by RT-PCR in HEK293T cells","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — protein microarray screen plus co-IP and ubiquitination assay, single lab","pmids":["23940030"],"is_preprint":false},{"year":2014,"finding":"FBXO25 is the substrate-recognition subunit of SCF(FBXO25) that targets HAX-1 for ubiquitin-proteasome degradation after apoptotic stress. PRKCD (protein kinase Cδ) phosphorylates both FBXO25 and HAX-1, directing nuclear FBXO25 to mitochondrial HAX-1. Monoallelic FBXO25 loss and stabilizing HAX1 phosphodegron mutations are found in primary MCL. FBXO25 re-expression in FBXO25-deleted MCL cells promotes cell death; HAX-1 phosphodegron mutant inhibits apoptosis. FBXO25 knockdown accelerates lymphoma in Eμ-Myc mice.","method":"Unbiased substrate screen; co-immunoprecipitation; ubiquitination assay; phosphorylation assay by PRKCD; genomic deletion mapping in human MCL; re-expression and knockdown in MCL cell lines; Eμ-Myc mouse and xenotransplant in vivo models","journal":"Nature medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (biochemical, genetic, in vivo), replicated across human patient samples and mouse models in a single rigorous study","pmids":["25419709"],"is_preprint":false},{"year":2015,"finding":"Fbxo25-mediated SCF ubiquitination pathway directly targets Tbx5 and Nkx2-5 for proteasomal degradation; Fbxo25 physically interacts with both transcription factors in vitro and in vivo. A dominant-negative Fbxo25 mutant (Fbxo25 1-236) blocks Tbx5 degradation and increases Tbx5 transcriptional activity. Silencing endogenous Fbxo25 increases Tbx5/Nkx2-5 mRNA and suppresses mESC-derived cardiomyocyte differentiation.","method":"Co-immunoprecipitation (in vitro and in vivo); proteasome inhibitor (MG132) rescue; temperature-sensitive ubiquitin system (ts20 cells); dominant-negative mutant expression; luciferase reporter assay; siRNA knockdown; mESC and hESC cardiomyocyte differentiation model; myocardial infarction mouse model","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods (co-IP, ts20 system, dominant-negative, reporter assay) in a single lab","pmids":["25725482"],"is_preprint":false},{"year":2017,"finding":"FBXO25 negatively regulates MAPK/ERK signaling by reducing ERK1/2 phosphorylation independently of MEK1/2. In FBXO25 knockout HAP1 cells, PMA-stimulated ERK1/2 activity and cell proliferation are enhanced compared to parental cells.","method":"FBXO25 overexpression; FBXO25 knockout cells (FBXO25KO HAP1); phospho-ERK1/2 immunoblot; cell proliferation assay; PMA stimulation","journal":"Archives of biochemistry and biophysics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with defined signaling readout, single lab, two complementary approaches","pmids":["28389297"],"is_preprint":false},{"year":2019,"finding":"FBXO25 is targeted for proteasome-dependent degradation by lncRNA ODIR1, which recruits CUL3 to facilitate FBXO25 degradation. FBXO25 increases mono-ubiquitination of H2BK120 (H2BK120ub), which promotes H3K4 trimethylation (H3K4me3), inducing chromatin opening at the OSX locus to drive osteogenic transcription. ODIR1-FBXO25 interaction was demonstrated by RNA-protein pulldown/co-IP.","method":"RNA immunoprecipitation; co-immunoprecipitation; ChIP assay; ubiquitination assay; siRNA knockdown and overexpression in hUC-MSCs; in vitro and in vivo osteogenic differentiation assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ChIP, ubiquitination, RNA-IP), single lab","pmids":["31827076"],"is_preprint":false},{"year":2020,"finding":"A replication study found that while FBXO25 interacts with ELK-1 in HEK293T cells and is active toward Hand1 and HAX1, FBXO25 does NOT promote ubiquitination or degradation of ELK-1, nor does it impact ELK-1 transcriptional activity. This negates the prior claim that FBXO25 is the E3 ligase for ELK-1.","method":"Co-immunoprecipitation; ubiquitination assay; protein turnover assay; RNA interference; gene expression analysis in HEK293T cells","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (co-IP, ubiquitination assay, turnover assay, RNAi), single lab contradicting prior report","pmids":["33428929"],"is_preprint":false},{"year":2020,"finding":"In cutaneous squamous cell carcinoma, FBXO25 interacts with Oct-1, leading to Oct-1 downregulation and consequent stabilization and upregulation of cyclin D1; FBXO25 silencing reduces tumor growth in association with reduced cyclin D1, and cyclin D1 overexpression rescues growth in FBXO25-deficient tumors.","method":"Stable FBXO25 knockdown and overexpression in SCC13 cells; co-immunoprecipitation (FBXO25-Oct-1); in vivo tumor growth assay; cyclin D1 rescue experiment; immunoblot","journal":"The Journal of investigative dermatology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP for interaction claim, partial mechanistic follow-up, single lab","pmids":["32335130"],"is_preprint":false}],"current_model":"FBXO25 is a nuclear F-box protein that functions as the substrate-recognition subunit of SCF(FBXO25) E3 ubiquitin ligase complexes; it is activated by PRKCD-mediated phosphorylation to ubiquitinate and degrade the pro-survival protein HAX-1 during apoptosis, ubiquitinates cardiac transcription factors (Nkx2-5, Isl1, Hand1, Tbx5) to regulate cardiomyocyte development, promotes H2BK120 mono-ubiquitination to regulate osteogenic gene expression, and negatively regulates MAPK/ERK signaling; it localizes to novel subnuclear FBXO25-associated nuclear domains (FAND) that are dynamically regulated by transcription and nuclear actin organization, and acts as a haploinsufficient tumor suppressor in mantle cell lymphoma."},"narrative":{"mechanistic_narrative":"FBXO25 is a nuclear F-box protein that serves as the substrate-recognition subunit of an SCF-type (Skp1–Cul1–Roc1) E3 ubiquitin ligase, assembling through an atypical serine residue in its F-box domain that mediates Skp1 binding [PMID:16278047, PMID:16714087]. The assembled SCF(FBXO25) complex is catalytically active and directs ubiquitin-dependent proteasomal turnover of a range of nuclear and signaling substrates. In the apoptotic program, PRKCD (PKCδ) phosphorylates both FBXO25 and the pro-survival protein HAX-1, redirecting nuclear FBXO25 to ubiquitinate and degrade HAX-1; monoallelic FBXO25 loss and stabilizing HAX1 phosphodegron mutations occur in mantle cell lymphoma, where FBXO25 re-expression promotes cell death and its knockdown accelerates Eμ-Myc-driven lymphoma, defining FBXO25 as a haploinsufficient tumor suppressor [PMID:25419709]. FBXO25 also targets cardiac transcription factors Nkx2-5, Isl1, Hand1, and Tbx5 for ubiquitination and degradation, thereby tuning cardiomyocyte differentiation [PMID:21596019, PMID:25725482], and promotes H2BK120 mono-ubiquitination to drive osteogenic gene expression, with its own levels controlled by lncRNA ODIR1-directed CUL3-dependent degradation [PMID:31827076]. FBXO25 negatively regulates MAPK/ERK signaling by suppressing ERK1/2 phosphorylation independently of MEK1/2 [PMID:28389297]. The protein concentrates in dynamic subnuclear FBXO25-associated nuclear domains (FAND) containing ubiquitin conjugates, 20S proteasome, and Skp1; these structures are dependent on ongoing transcription and on nuclear β-actin organization, and FBXO25 ligase activity prevents nuclear polyglutamine huntingtin aggregation [PMID:18287534, PMID:20473970]. A prior assignment of ELK-1 as an FBXO25 substrate was contradicted by a replication study that confirmed FBXO25–ELK-1 interaction but found no ELK-1 ubiquitination or degradation [PMID:23940030, PMID:33428929].","teleology":[{"year":2005,"claim":"Establishing whether FBXO25 is a bona fide F-box protein defined its molecular identity as an SCF ligase adaptor rather than an orphan nuclear protein.","evidence":"Co-IP with Skp1/Cul1 and F-box serine mutagenesis, with nuclear localization and brain expression by immunochemistry and RT-PCR","pmids":["16278047"],"confidence":"Medium","gaps":["No substrate identified at this stage","Functional ligase activity not yet demonstrated"]},{"year":2006,"claim":"Demonstrating that FBXO25 assembles a productive SCF complex with in vitro ligase activity confirmed it is an enzymatically functional ligase, distinct in tissue and atrophy regulation from its paralog atrogin-1.","evidence":"Co-IP plus in vitro ubiquitin ligase assay; RT-PCR tissue panel; mouse fasting/dexamethasone/diabetes muscle-atrophy models","pmids":["16714087"],"confidence":"Medium","gaps":["No physiological substrate identified","Activity shown only in vitro"]},{"year":2008,"claim":"Identifying that FBXO25 concentrates in transcription-sensitive subnuclear FAND containing proteasome and ubiquitin conjugates placed its activity in a defined nuclear compartment and linked it to protein-aggregation control.","evidence":"Confocal immunofluorescence, biochemical fractionation, actinomycin D/heat-shock perturbation, and huntingtin aggregation assay in HEK293","pmids":["18287534"],"confidence":"Medium","gaps":["Molecular function of FAND undefined","Endogenous substrate degraded in FAND not identified"]},{"year":2010,"claim":"Mapping the FBXO25 interactome and the β-actin dependence of FAND connected its compartmentalization to nuclear actin and transcriptional machinery.","evidence":"Two-step affinity purification MS, two-hybrid screen, β-actin co-IP, actin polymerization inhibitors, in vitro RNA Pol II transcription assay","pmids":["20473970"],"confidence":"Medium","gaps":["132 candidate partners mostly unvalidated","Direct ubiquitination substrates among partners not established"]},{"year":2011,"claim":"Identifying cardiac transcription factors as direct substrates assigned FBXO25 a developmental role in regulating cardiomyocyte transcription factor abundance.","evidence":"Ubiquitination assays, MG132 rescue, immunofluorescence, and immunoblot in cardiomyocytes and ESC differentiation model","pmids":["21596019"],"confidence":"Medium","gaps":["In vivo cardiac requirement not tested by genetic loss","Recruitment determinants/degrons on substrates undefined"]},{"year":2013,"claim":"Assigning ELK-1 as an SCF(FBXO25) substrate proposed a role in dampening immediate-early MAPK target gene induction.","evidence":"Protein microarray ubiquitination screen, co-IP, ubiquitination assay, cycloheximide chase, and RT-PCR in HEK293T","pmids":["23940030"],"confidence":"Medium","gaps":["Later contradicted for ELK-1 ubiquitination","Endogenous-level effects not established"]},{"year":2014,"claim":"Defining the PRKCD–FBXO25–HAX-1 axis explained how an apoptotic kinase signal is converted into degradation of a survival factor, and established FBXO25 as a haploinsufficient tumor suppressor in mantle cell lymphoma.","evidence":"Unbiased substrate screen, co-IP, ubiquitination and PRKCD phosphorylation assays, genomic deletion mapping in human MCL, re-expression/knockdown in MCL lines, and Eμ-Myc and xenotransplant mouse models","pmids":["25419709"],"confidence":"High","gaps":["Structural basis of phospho-directed nuclear-to-mitochondrial substrate handoff unresolved","Full substrate spectrum in lymphoma not defined"]},{"year":2015,"claim":"Extending substrate degradation to Tbx5 and Nkx2-5 with a dominant-negative mutant established that FBXO25 ubiquitin-proteasome activity restrains cardiac transcription factor activity during cardiomyocyte differentiation.","evidence":"Co-IP, MG132 rescue, ts20 temperature-sensitive ubiquitin system, dominant-negative mutant, luciferase reporter, siRNA, mESC/hESC differentiation and myocardial infarction models","pmids":["25725482"],"confidence":"Medium","gaps":["In vivo developmental phenotype of FBXO25 null heart not shown","Regulation of FBXO25 activity in cardiac context unclear"]},{"year":2017,"claim":"Showing FBXO25 loss enhances PMA-induced ERK1/2 phosphorylation independently of MEK1/2 placed FBXO25 as a negative regulator of MAPK/ERK output and proliferation.","evidence":"FBXO25 overexpression and KO HAP1 cells, phospho-ERK1/2 immunoblot, PMA stimulation, proliferation assay","pmids":["28389297"],"confidence":"Medium","gaps":["Direct ubiquitination substrate mediating ERK suppression not identified","MEK-independent mechanism undefined"]},{"year":2019,"claim":"Linking FBXO25 to H2BK120 mono-ubiquitination and its own ODIR1/CUL3-directed degradation connected FBXO25 to chromatin-based control of osteogenic transcription and revealed a layer of post-translational regulation of FBXO25 itself.","evidence":"RNA-IP, co-IP, ChIP, ubiquitination assay, siRNA/overexpression in hUC-MSCs, and in vitro/in vivo osteogenic differentiation","pmids":["31827076"],"confidence":"Medium","gaps":["Mechanism by which FBXO25 promotes H2BK120ub (direct vs indirect) unclear","Generality beyond OSX locus untested"]},{"year":2020,"claim":"A direct replication corrected the substrate record by confirming FBXO25–ELK-1 binding but excluding ELK-1 as a degradation substrate, sharpening the bona fide substrate set.","evidence":"Co-IP, ubiquitination assay, protein turnover assay, RNAi, and gene expression analysis in HEK293T","pmids":["33428929"],"confidence":"Medium","gaps":["Functional consequence of the retained ELK-1 interaction unknown","Does not address other proposed substrates"]},{"year":2020,"claim":"Identifying an FBXO25–Oct-1–cyclin D1 axis proposed a context-dependent tumor-promoting role in cutaneous squamous cell carcinoma, contrasting its tumor-suppressor role in lymphoma.","evidence":"FBXO25 knockdown/overexpression in SCC13 cells, FBXO25–Oct-1 co-IP, in vivo tumor growth, and cyclin D1 rescue","pmids":["32335130"],"confidence":"Low","gaps":["Single Co-IP without reciprocal/ubiquitination validation of Oct-1 as substrate","Tissue-context basis for opposite cancer roles unexplained"]},{"year":null,"claim":"How a single nuclear SCF(FBXO25) adaptor selects among diverse substrates across apoptotic, cardiac, osteogenic, and signaling contexts — and how upstream signals and FAND localization gate this selection — remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of substrate or degron recognition","Determinants of context-specific substrate choice unknown","Physiological loss-of-function phenotype across tissues not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4,5,6,7,9]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,1,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,2,4]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[2,3]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,6]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[6]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[8]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4,7]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[9]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[6,11]}],"complexes":["SCF(FBXO25) (Skp1-Cul1-Roc1-FBXO25)"],"partners":["SKP1","CUL1","RBX1","HAX1","PRKCD","ACTB","TBX5","NKX2-5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8TCJ0","full_name":"F-box only protein 25","aliases":[],"length_aa":367,"mass_kda":43.3,"function":"Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. May play a role in accumulation of expanded polyglutamine (polyQ) protein huntingtin (HTT) (By similarity)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8TCJ0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FBXO25","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FBXO25","total_profiled":1310},"omim":[{"mim_id":"609098","title":"F-BOX ONLY PROTEIN 25; FBXO25","url":"https://www.omim.org/entry/609098"},{"mim_id":"606604","title":"F-BOX ONLY PROTEIN 32; FBXO32","url":"https://www.omim.org/entry/606604"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"testis","ntpm":91.6}],"url":"https://www.proteinatlas.org/search/FBXO25"},"hgnc":{"alias_symbol":["FBX25"],"prev_symbol":[]},"alphafold":{"accession":"Q8TCJ0","domains":[{"cath_id":"-","chopping":"93-216","consensus_level":"high","plddt":87.2114,"start":93,"end":216},{"cath_id":"1.20.1280.50","chopping":"229-307","consensus_level":"medium","plddt":90.1115,"start":229,"end":307},{"cath_id":"-","chopping":"318-358","consensus_level":"medium","plddt":81.6022,"start":318,"end":358}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TCJ0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TCJ0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TCJ0-F1-predicted_aligned_error_v6.png","plddt_mean":76.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FBXO25","jax_strain_url":"https://www.jax.org/strain/search?query=FBXO25"},"sequence":{"accession":"Q8TCJ0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8TCJ0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8TCJ0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TCJ0"}},"corpus_meta":[{"pmid":"31827076","id":"PMC_31827076","title":"LncRNA ODIR1 inhibits osteogenic differentiation of hUC-MSCs through the FBXO25/H2BK120ub/H3K4me3/OSX axis.","date":"2019","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/31827076","citation_count":70,"is_preprint":false},{"pmid":"25419709","id":"PMC_25419709","title":"Disruption of the PRKCD-FBXO25-HAX-1 axis attenuates the apoptotic response and drives lymphomagenesis.","date":"2014","source":"Nature medicine","url":"https://pubmed.ncbi.nlm.nih.gov/25419709","citation_count":53,"is_preprint":false},{"pmid":"20601059","id":"PMC_20601059","title":"Molecular characterization of atrogin-1/F-box protein-32 (FBXO32) and F-box protein-25 (FBXO25) in rainbow trout (Oncorhynchus mykiss): Expression across tissues in response to feed deprivation.","date":"2010","source":"Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/20601059","citation_count":43,"is_preprint":false},{"pmid":"21596019","id":"PMC_21596019","title":"A novel Fbxo25 acts as an E3 ligase for destructing cardiac specific transcription factors.","date":"2011","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/21596019","citation_count":26,"is_preprint":false},{"pmid":"16278047","id":"PMC_16278047","title":"Characterization of FBX25, encoding a novel brain-expressed F-box protein.","date":"2005","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/16278047","citation_count":20,"is_preprint":false},{"pmid":"23940030","id":"PMC_23940030","title":"The F-box protein FBXO25 promotes the proteasome-dependent degradation of ELK-1 protein.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23940030","citation_count":16,"is_preprint":false},{"pmid":"18287534","id":"PMC_18287534","title":"FBXO25-associated nuclear domains: a novel subnuclear structure.","date":"2008","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/18287534","citation_count":16,"is_preprint":false},{"pmid":"25725482","id":"PMC_25725482","title":"Fbxo25 controls Tbx5 and Nkx2-5 transcriptional activity to regulate cardiomyocyte development.","date":"2015","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/25725482","citation_count":15,"is_preprint":false},{"pmid":"16714087","id":"PMC_16714087","title":"FBXO25, an F-box protein homologue of atrogin-1, is not induced in atrophying muscle.","date":"2006","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/16714087","citation_count":13,"is_preprint":false},{"pmid":"32335130","id":"PMC_32335130","title":"FBXO25 Promotes Cutaneous Squamous Cell Carcinoma Growth and Metastasis through Cyclin D1.","date":"2020","source":"The Journal of investigative dermatology","url":"https://pubmed.ncbi.nlm.nih.gov/32335130","citation_count":10,"is_preprint":false},{"pmid":"27596142","id":"PMC_27596142","title":"FBXO25 promotes cell proliferation, invasion, and migration of NSCLC.","date":"2016","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/27596142","citation_count":9,"is_preprint":false},{"pmid":"28389297","id":"PMC_28389297","title":"FBXO25 regulates MAPK signaling pathway through inhibition of ERK1/2 phosphorylation.","date":"2017","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/28389297","citation_count":8,"is_preprint":false},{"pmid":"20473970","id":"PMC_20473970","title":"Identification of FBXO25-interacting proteins using an integrated proteomics approach.","date":"2010","source":"Proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/20473970","citation_count":8,"is_preprint":false},{"pmid":"31849056","id":"PMC_31849056","title":"From man to fly - convergent evidence links FBXO25 to ADHD and comorbid psychiatric phenotypes.","date":"2019","source":"Journal of child psychology and psychiatry, and allied disciplines","url":"https://pubmed.ncbi.nlm.nih.gov/31849056","citation_count":8,"is_preprint":false},{"pmid":"33428929","id":"PMC_33428929","title":"ELK-1 ubiquitination status and transcriptional activity are modulated independently of F-Box protein FBXO25.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/33428929","citation_count":4,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9265,"output_tokens":3618,"usd":0.041032,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11098,"output_tokens":4464,"usd":0.083545,"stage2_stop_reason":"end_turn"},"total_usd":0.124577,"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\": 2005,\n      \"finding\": \"FBXO25 (hFBX25) was established as an F-box protein that interacts with Skp1 and Cul1, forming part of an SCF-type ubiquitin ligase complex. An atypical serine residue in the F-box domain was identified as crucial for hFBX25-Skp1 binding. FBXO25 localizes to the nucleus and is strongly expressed in brain tissue.\",\n      \"method\": \"Interaction verified by co-immunoprecipitation; F-box domain mutagenesis (serine residue); subcellular localization by immunochemistry; tissue expression by RT-PCR/immunoblot\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with mutagenesis in a single focused study, two orthogonal methods\",\n      \"pmids\": [\"16278047\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"FBXO25 contains a functional F-box domain that binds Skp1 and thereby assembles with Roc1 and Cul1 into a productive SCF complex with ubiquitin ligase activity in vitro. FBXO25 is expressed in brain, kidney, and intestine but not striated muscle, and is not induced in atrophying muscle unlike its paralog atrogin-1.\",\n      \"method\": \"Co-immunoprecipitation; in vitro ubiquitin ligase activity assay; RT-PCR tissue expression; mouse fasting, dexamethasone, and streptozotocin-diabetes models\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro ligase assay plus co-IP, single lab, two orthogonal methods\",\n      \"pmids\": [\"16714087\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Endogenous FBXO25 accumulates in novel dot-like subnuclear structures (FBXO25-associated nuclear domains, FAND) that are distinct from clastosomes and contain ubiquitin conjugates, 20S proteasome, and Skp1. FAND are dynamic and disrupted by transcription inhibition (actinomycin D) or heat shock. FBXO25-dependent ubiquitin ligase activity in the nucleus prevents aggregation of polyglutamine-containing huntingtin in HEK293 cells.\",\n      \"method\": \"Confocal immunofluorescence with affinity-purified antibodies; biochemical fractionation; actinomycin D/heat-shock perturbation; huntingtin aggregation assay in HEK293 cells\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiments with functional consequence, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"18287534\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Integrated proteomics (two-step affinity purification + MS and two-hybrid screen) identified 132 potential FBXO25-interacting partners. Beta-actin physically interacts via its N-terminus with FBXO25 and is enriched in FAND; inhibitors of actin polymerization disrupt FAND, indicating nuclear actin organization regulates these compartments. FBXO25 antibodies interfered with RNA polymerase II transcription in vitro.\",\n      \"method\": \"Two-step affinity purification followed by MS; two-hybrid screen; co-immunoprecipitation (beta-actin); actin polymerization inhibitors; in vitro RNA Pol II transcription assay with antibody interference\",\n      \"journal\": \"Proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal MS interactome plus functional in vitro assay, single lab\",\n      \"pmids\": [\"20473970\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Fbxo25 acts as an E3 ubiquitin ligase for cardiac transcription factors: it directly ubiquitinates Nkx2-5, Isl1, and Hand1, and facilitates proteasome-dependent degradation of Nkx2-5, Isl1, Hand1, and Mef2C. Fbxo25 is expressed in cardiomyocyte nuclei with higher levels in fetal versus adult heart, and its expression increases during ESC-derived cardiomyocyte development.\",\n      \"method\": \"Ubiquitination assays; proteasome inhibitor (MG132) rescue; immunofluorescence localization; immunoblot in cardiomyocytes and ESC differentiation model\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination assay plus degradation rescue, single lab, two methods\",\n      \"pmids\": [\"21596019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"FBXO25 interacts with and mediates ubiquitination and proteasomal degradation of ELK-1 in HEK293T cells, functioning as the substrate-recognition subunit of SCF(FBXO25). FBXO25 overexpression suppresses induction of ELK-1 target genes c-fos and egr-1 in response to phorbol ester.\",\n      \"method\": \"Human protein microarray ubiquitination screen; co-immunoprecipitation; ubiquitination assay; cycloheximide chase; gene expression by RT-PCR in HEK293T cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — protein microarray screen plus co-IP and ubiquitination assay, single lab\",\n      \"pmids\": [\"23940030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"FBXO25 is the substrate-recognition subunit of SCF(FBXO25) that targets HAX-1 for ubiquitin-proteasome degradation after apoptotic stress. PRKCD (protein kinase Cδ) phosphorylates both FBXO25 and HAX-1, directing nuclear FBXO25 to mitochondrial HAX-1. Monoallelic FBXO25 loss and stabilizing HAX1 phosphodegron mutations are found in primary MCL. FBXO25 re-expression in FBXO25-deleted MCL cells promotes cell death; HAX-1 phosphodegron mutant inhibits apoptosis. FBXO25 knockdown accelerates lymphoma in Eμ-Myc mice.\",\n      \"method\": \"Unbiased substrate screen; co-immunoprecipitation; ubiquitination assay; phosphorylation assay by PRKCD; genomic deletion mapping in human MCL; re-expression and knockdown in MCL cell lines; Eμ-Myc mouse and xenotransplant in vivo models\",\n      \"journal\": \"Nature medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (biochemical, genetic, in vivo), replicated across human patient samples and mouse models in a single rigorous study\",\n      \"pmids\": [\"25419709\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Fbxo25-mediated SCF ubiquitination pathway directly targets Tbx5 and Nkx2-5 for proteasomal degradation; Fbxo25 physically interacts with both transcription factors in vitro and in vivo. A dominant-negative Fbxo25 mutant (Fbxo25 1-236) blocks Tbx5 degradation and increases Tbx5 transcriptional activity. Silencing endogenous Fbxo25 increases Tbx5/Nkx2-5 mRNA and suppresses mESC-derived cardiomyocyte differentiation.\",\n      \"method\": \"Co-immunoprecipitation (in vitro and in vivo); proteasome inhibitor (MG132) rescue; temperature-sensitive ubiquitin system (ts20 cells); dominant-negative mutant expression; luciferase reporter assay; siRNA knockdown; mESC and hESC cardiomyocyte differentiation model; myocardial infarction mouse model\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods (co-IP, ts20 system, dominant-negative, reporter assay) in a single lab\",\n      \"pmids\": [\"25725482\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"FBXO25 negatively regulates MAPK/ERK signaling by reducing ERK1/2 phosphorylation independently of MEK1/2. In FBXO25 knockout HAP1 cells, PMA-stimulated ERK1/2 activity and cell proliferation are enhanced compared to parental cells.\",\n      \"method\": \"FBXO25 overexpression; FBXO25 knockout cells (FBXO25KO HAP1); phospho-ERK1/2 immunoblot; cell proliferation assay; PMA stimulation\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with defined signaling readout, single lab, two complementary approaches\",\n      \"pmids\": [\"28389297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FBXO25 is targeted for proteasome-dependent degradation by lncRNA ODIR1, which recruits CUL3 to facilitate FBXO25 degradation. FBXO25 increases mono-ubiquitination of H2BK120 (H2BK120ub), which promotes H3K4 trimethylation (H3K4me3), inducing chromatin opening at the OSX locus to drive osteogenic transcription. ODIR1-FBXO25 interaction was demonstrated by RNA-protein pulldown/co-IP.\",\n      \"method\": \"RNA immunoprecipitation; co-immunoprecipitation; ChIP assay; ubiquitination assay; siRNA knockdown and overexpression in hUC-MSCs; in vitro and in vivo osteogenic differentiation assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ChIP, ubiquitination, RNA-IP), single lab\",\n      \"pmids\": [\"31827076\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"A replication study found that while FBXO25 interacts with ELK-1 in HEK293T cells and is active toward Hand1 and HAX1, FBXO25 does NOT promote ubiquitination or degradation of ELK-1, nor does it impact ELK-1 transcriptional activity. This negates the prior claim that FBXO25 is the E3 ligase for ELK-1.\",\n      \"method\": \"Co-immunoprecipitation; ubiquitination assay; protein turnover assay; RNA interference; gene expression analysis in HEK293T cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (co-IP, ubiquitination assay, turnover assay, RNAi), single lab contradicting prior report\",\n      \"pmids\": [\"33428929\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In cutaneous squamous cell carcinoma, FBXO25 interacts with Oct-1, leading to Oct-1 downregulation and consequent stabilization and upregulation of cyclin D1; FBXO25 silencing reduces tumor growth in association with reduced cyclin D1, and cyclin D1 overexpression rescues growth in FBXO25-deficient tumors.\",\n      \"method\": \"Stable FBXO25 knockdown and overexpression in SCC13 cells; co-immunoprecipitation (FBXO25-Oct-1); in vivo tumor growth assay; cyclin D1 rescue experiment; immunoblot\",\n      \"journal\": \"The Journal of investigative dermatology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP for interaction claim, partial mechanistic follow-up, single lab\",\n      \"pmids\": [\"32335130\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FBXO25 is a nuclear F-box protein that functions as the substrate-recognition subunit of SCF(FBXO25) E3 ubiquitin ligase complexes; it is activated by PRKCD-mediated phosphorylation to ubiquitinate and degrade the pro-survival protein HAX-1 during apoptosis, ubiquitinates cardiac transcription factors (Nkx2-5, Isl1, Hand1, Tbx5) to regulate cardiomyocyte development, promotes H2BK120 mono-ubiquitination to regulate osteogenic gene expression, and negatively regulates MAPK/ERK signaling; it localizes to novel subnuclear FBXO25-associated nuclear domains (FAND) that are dynamically regulated by transcription and nuclear actin organization, and acts as a haploinsufficient tumor suppressor in mantle cell lymphoma.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FBXO25 is a nuclear F-box protein that serves as the substrate-recognition subunit of an SCF-type (Skp1–Cul1–Roc1) E3 ubiquitin ligase, assembling through an atypical serine residue in its F-box domain that mediates Skp1 binding [#0, #1]. The assembled SCF(FBXO25) complex is catalytically active and directs ubiquitin-dependent proteasomal turnover of a range of nuclear and signaling substrates. In the apoptotic program, PRKCD (PKCδ) phosphorylates both FBXO25 and the pro-survival protein HAX-1, redirecting nuclear FBXO25 to ubiquitinate and degrade HAX-1; monoallelic FBXO25 loss and stabilizing HAX1 phosphodegron mutations occur in mantle cell lymphoma, where FBXO25 re-expression promotes cell death and its knockdown accelerates Eμ-Myc-driven lymphoma, defining FBXO25 as a haploinsufficient tumor suppressor [#6]. FBXO25 also targets cardiac transcription factors Nkx2-5, Isl1, Hand1, and Tbx5 for ubiquitination and degradation, thereby tuning cardiomyocyte differentiation [#4, #7], and promotes H2BK120 mono-ubiquitination to drive osteogenic gene expression, with its own levels controlled by lncRNA ODIR1-directed CUL3-dependent degradation [#9]. FBXO25 negatively regulates MAPK/ERK signaling by suppressing ERK1/2 phosphorylation independently of MEK1/2 [#8]. The protein concentrates in dynamic subnuclear FBXO25-associated nuclear domains (FAND) containing ubiquitin conjugates, 20S proteasome, and Skp1; these structures are dependent on ongoing transcription and on nuclear β-actin organization, and FBXO25 ligase activity prevents nuclear polyglutamine huntingtin aggregation [#2, #3]. A prior assignment of ELK-1 as an FBXO25 substrate was contradicted by a replication study that confirmed FBXO25–ELK-1 interaction but found no ELK-1 ubiquitination or degradation [#5, #10].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Establishing whether FBXO25 is a bona fide F-box protein defined its molecular identity as an SCF ligase adaptor rather than an orphan nuclear protein.\",\n      \"evidence\": \"Co-IP with Skp1/Cul1 and F-box serine mutagenesis, with nuclear localization and brain expression by immunochemistry and RT-PCR\",\n      \"pmids\": [\"16278047\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No substrate identified at this stage\", \"Functional ligase activity not yet demonstrated\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstrating that FBXO25 assembles a productive SCF complex with in vitro ligase activity confirmed it is an enzymatically functional ligase, distinct in tissue and atrophy regulation from its paralog atrogin-1.\",\n      \"evidence\": \"Co-IP plus in vitro ubiquitin ligase assay; RT-PCR tissue panel; mouse fasting/dexamethasone/diabetes muscle-atrophy models\",\n      \"pmids\": [\"16714087\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No physiological substrate identified\", \"Activity shown only in vitro\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identifying that FBXO25 concentrates in transcription-sensitive subnuclear FAND containing proteasome and ubiquitin conjugates placed its activity in a defined nuclear compartment and linked it to protein-aggregation control.\",\n      \"evidence\": \"Confocal immunofluorescence, biochemical fractionation, actinomycin D/heat-shock perturbation, and huntingtin aggregation assay in HEK293\",\n      \"pmids\": [\"18287534\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular function of FAND undefined\", \"Endogenous substrate degraded in FAND not identified\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Mapping the FBXO25 interactome and the β-actin dependence of FAND connected its compartmentalization to nuclear actin and transcriptional machinery.\",\n      \"evidence\": \"Two-step affinity purification MS, two-hybrid screen, β-actin co-IP, actin polymerization inhibitors, in vitro RNA Pol II transcription assay\",\n      \"pmids\": [\"20473970\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"132 candidate partners mostly unvalidated\", \"Direct ubiquitination substrates among partners not established\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identifying cardiac transcription factors as direct substrates assigned FBXO25 a developmental role in regulating cardiomyocyte transcription factor abundance.\",\n      \"evidence\": \"Ubiquitination assays, MG132 rescue, immunofluorescence, and immunoblot in cardiomyocytes and ESC differentiation model\",\n      \"pmids\": [\"21596019\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo cardiac requirement not tested by genetic loss\", \"Recruitment determinants/degrons on substrates undefined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Assigning ELK-1 as an SCF(FBXO25) substrate proposed a role in dampening immediate-early MAPK target gene induction.\",\n      \"evidence\": \"Protein microarray ubiquitination screen, co-IP, ubiquitination assay, cycloheximide chase, and RT-PCR in HEK293T\",\n      \"pmids\": [\"23940030\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Later contradicted for ELK-1 ubiquitination\", \"Endogenous-level effects not established\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defining the PRKCD–FBXO25–HAX-1 axis explained how an apoptotic kinase signal is converted into degradation of a survival factor, and established FBXO25 as a haploinsufficient tumor suppressor in mantle cell lymphoma.\",\n      \"evidence\": \"Unbiased substrate screen, co-IP, ubiquitination and PRKCD phosphorylation assays, genomic deletion mapping in human MCL, re-expression/knockdown in MCL lines, and Eμ-Myc and xenotransplant mouse models\",\n      \"pmids\": [\"25419709\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of phospho-directed nuclear-to-mitochondrial substrate handoff unresolved\", \"Full substrate spectrum in lymphoma not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Extending substrate degradation to Tbx5 and Nkx2-5 with a dominant-negative mutant established that FBXO25 ubiquitin-proteasome activity restrains cardiac transcription factor activity during cardiomyocyte differentiation.\",\n      \"evidence\": \"Co-IP, MG132 rescue, ts20 temperature-sensitive ubiquitin system, dominant-negative mutant, luciferase reporter, siRNA, mESC/hESC differentiation and myocardial infarction models\",\n      \"pmids\": [\"25725482\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo developmental phenotype of FBXO25 null heart not shown\", \"Regulation of FBXO25 activity in cardiac context unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showing FBXO25 loss enhances PMA-induced ERK1/2 phosphorylation independently of MEK1/2 placed FBXO25 as a negative regulator of MAPK/ERK output and proliferation.\",\n      \"evidence\": \"FBXO25 overexpression and KO HAP1 cells, phospho-ERK1/2 immunoblot, PMA stimulation, proliferation assay\",\n      \"pmids\": [\"28389297\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitination substrate mediating ERK suppression not identified\", \"MEK-independent mechanism undefined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Linking FBXO25 to H2BK120 mono-ubiquitination and its own ODIR1/CUL3-directed degradation connected FBXO25 to chromatin-based control of osteogenic transcription and revealed a layer of post-translational regulation of FBXO25 itself.\",\n      \"evidence\": \"RNA-IP, co-IP, ChIP, ubiquitination assay, siRNA/overexpression in hUC-MSCs, and in vitro/in vivo osteogenic differentiation\",\n      \"pmids\": [\"31827076\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which FBXO25 promotes H2BK120ub (direct vs indirect) unclear\", \"Generality beyond OSX locus untested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"A direct replication corrected the substrate record by confirming FBXO25–ELK-1 binding but excluding ELK-1 as a degradation substrate, sharpening the bona fide substrate set.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, protein turnover assay, RNAi, and gene expression analysis in HEK293T\",\n      \"pmids\": [\"33428929\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the retained ELK-1 interaction unknown\", \"Does not address other proposed substrates\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identifying an FBXO25–Oct-1–cyclin D1 axis proposed a context-dependent tumor-promoting role in cutaneous squamous cell carcinoma, contrasting its tumor-suppressor role in lymphoma.\",\n      \"evidence\": \"FBXO25 knockdown/overexpression in SCC13 cells, FBXO25–Oct-1 co-IP, in vivo tumor growth, and cyclin D1 rescue\",\n      \"pmids\": [\"32335130\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP without reciprocal/ubiquitination validation of Oct-1 as substrate\", \"Tissue-context basis for opposite cancer roles unexplained\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single nuclear SCF(FBXO25) adaptor selects among diverse substrates across apoptotic, cardiac, osteogenic, and signaling contexts — and how upstream signals and FAND localization gate this selection — remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of substrate or degron recognition\", \"Determinants of context-specific substrate choice unknown\", \"Physiological loss-of-function phenotype across tissues not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4, 5, 6, 7, 9]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2, 4]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [6, 11]}\n    ],\n    \"complexes\": [\"SCF(FBXO25) (Skp1-Cul1-Roc1-FBXO25)\"],\n    \"partners\": [\"SKP1\", \"CUL1\", \"RBX1\", \"HAX1\", \"PRKCD\", \"ACTB\", \"TBX5\", \"NKX2-5\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}