{"gene":"UBE2Q1","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2015,"finding":"UBE2Q1 physically interacts with p53 protein (demonstrated by co-immunoprecipitation and GST pull-down in MDA-MB-468 breast cancer cells), and overexpression of UBE2Q1 reduces p53 protein levels, consistent with UBE2Q1-mediated ubiquitination and proteasomal degradation of p53.","method":"Co-immunoprecipitation, GST pull-down, Western blot after overexpression","journal":"Asian Pacific journal of cancer prevention : APJCP","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal in vivo and in vitro binding assays (Co-IP and GST pull-down), single lab, two orthogonal binding methods; degradation mechanism inferred but not directly demonstrated with ubiquitination assay","pmids":["25987028"],"is_preprint":false},{"year":2013,"finding":"UBE2Q1 knockdown in PC12 neuronal cells increases p53 protein levels, while UBE2Q1 overexpression reduces p53 levels, linking UBE2Q1 to regulation of p53 abundance and downstream apoptotic signaling (increased bax, p21, active caspase-3 upon TBI-associated downregulation of UBE2Q1).","method":"siRNA knockdown and overexpression in PC12 cells, Western blot for p53/bax/p21/caspase-3, immunohistochemistry and immunofluorescence in rat brain cortex","journal":"Journal of neuroscience research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function and gain-of-function with defined molecular readout (p53 levels), single lab, two complementary approaches (KD and OE)","pmids":["24166684"],"is_preprint":false},{"year":2013,"finding":"UBE2Q1 protein is expressed predominantly in the nucleus of neurons (with minority expression in astrocytes) in normal rat brain cortex, as established by double-immunofluorescence staining.","method":"Double-immunofluorescence staining in rat brain cortex","journal":"Journal of neuroscience research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single localization experiment in one tissue, single lab, no functional consequence directly tied to nuclear localization","pmids":["24166684"],"is_preprint":false},{"year":2013,"finding":"Mouse Ube2q1 knockout females exhibit pleiotropic reproductive defects including altered oestrus cycle, abnormal sexual behaviour, reduced offspring care, increased embryonic lethality, and decreased embryo implantation capacity, establishing a required role for UBE2Q1 in female fertility. Expression is induced in the uterus during pregnancy.","method":"Knockout mouse model (gene targeting), reproductive phenotype analysis, expression analysis by in situ hybridization/RT-PCR","journal":"Reproduction (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO mouse with defined multi-parameter reproductive phenotype; uterine expression verified by expression analysis; multiple orthogonal phenotypic readouts in a single rigorous study","pmids":["23108111"],"is_preprint":false},{"year":2013,"finding":"UBE2Q1 is implicated in regulation of membrane B4GALT1 (beta-1,4-galactosyltransferase 1) protein, based on prior work cited in the Ube2q1 knockout paper.","method":"Referenced as prior finding in knockout paper (no direct experimental detail provided in this abstract)","journal":"Reproduction (Cambridge, England)","confidence":"Low","confidence_rationale":"Tier 4 / Weak — referenced as an established finding without experimental detail provided in the abstract; cannot evaluate methodology","pmids":["23108111"],"is_preprint":false},{"year":2023,"finding":"Molecular docking and co-immunoprecipitation in stably transfected SW1116 colorectal cancer cells indicate that the UBC domain of UBE2Q1 has high binding affinity for B4GALT1 and p53 (both tetramerization and DNA-binding domains), identifying hot-spot interaction regions.","method":"Co-immunoprecipitation with silver staining, molecular docking (MOE software) of UBC domain (PDB: 2QGX) against B4GALT1 (2AGD) and p53 (1AIE, 1GZH)","journal":"Protein and peptide letters","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-IP in a single cell line and computational docking without functional ubiquitination assay validation; single lab","pmids":["37198983"],"is_preprint":false},{"year":2017,"finding":"UBE2Q1 knockdown in HCC cell lines reduces cell proliferation, promotes apoptosis via induction of GADD45α, suppresses cell migration and invasion through regulation of EMT, and suppresses orthotopic tumorigenicity in vivo. UBE2Q1 activity is linked to the β-catenin-EGFR-PI3K-Akt-mTOR signaling pathway.","method":"siRNA knockdown, in vitro proliferation/apoptosis/migration/invasion assays, in vivo orthotopic xenograft model, Western blot for pathway components","journal":"Molecular carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with multiple phenotypic readouts in vitro and in vivo, pathway Western blot, single lab","pmids":["29027712"],"is_preprint":false},{"year":2016,"finding":"Stable overexpression of UBE2Q1 in SW1116 colorectal cancer cells increases cell proliferation, colony formation, motility, and causes a decrease in G0/G1 phase accumulation (shift toward S phase), demonstrating a direct role of UBE2Q1 in cell cycle progression.","method":"Stable transfection with pCMV6-AN-GFP-UBE2Q1, MTT assay, crystal violet colony assay, flow cytometry cell cycle analysis, wound healing assay","journal":"Oncology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gain-of-function with multiple orthogonal cellular assays, single lab","pmids":["27602158"],"is_preprint":false},{"year":2024,"finding":"UBE2Q1 interacts with DDX3 in BCR::ABL T315I mutation CML cells and regulates DDX3 ubiquitination; Bortezomib targets UBE2Q1 and reduces its protein level, leading to apoptosis via ROS production, mitochondrial membrane potential collapse, and cytochrome C release.","method":"Co-immunoprecipitation (UBE2Q1-DDX3 interaction), Western blot, cell viability assays, flow cytometry for ROS/mitochondrial potential, in vivo xenograft model","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP demonstrating UBE2Q1-DDX3 interaction with ubiquitination regulation, in vitro and in vivo functional data, single lab","pmids":["39454411"],"is_preprint":false},{"year":2022,"finding":"UBE2Q1 stabilizes β-catenin protein, which in turn activates HIF-1α to enhance hypoxia-driven glycolysis (Warburg effect) in colorectal cancer cells; this pathway is downstream of miR-338-3p targeting of UBE2Q1.","method":"siRNA knockdown and overexpression, luciferase reporter (for miR-338-3p/UBE2Q1 axis), Western blot for β-catenin and HIF-1α, glycolysis assays in hypoxia, in vivo tumor model","journal":"Bioengineered","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional rescue experiments with multiple readouts, in vitro and in vivo, single lab; β-catenin stabilization by UBE2Q1 inferred from OE/KD without direct ubiquitination assay","pmids":["35156520"],"is_preprint":false},{"year":2021,"finding":"miR-338-3p directly targets the 3'-UTR of UBE2Q1 mRNA (luciferase reporter assay), negatively regulating its expression; overexpression of UBE2Q1 rescues miR-338-3p-mediated inhibition of autophagy via the AKT/mTOR pathway in nasal epithelial cells exposed to PM2.5.","method":"Luciferase reporter assay (miR-338-3p binding to UBE2Q1 3'-UTR), Western blot, overexpression rescue experiments, in vivo AR rat model","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct 3'-UTR reporter validation plus functional rescue, in vitro and in vivo, single lab","pmids":["33770685"],"is_preprint":false}],"current_model":"UBE2Q1 is a E2 ubiquitin-conjugating enzyme (containing a UBC domain and RWD domain) that physically interacts with and promotes ubiquitination/degradation of p53 and interacts with B4GALT1 and DDX3; it stabilizes β-catenin to activate HIF-1α-driven glycolysis and regulates the β-catenin-EGFR-PI3K-Akt-mTOR signaling axis, promoting cell cycle progression (S-phase entry), proliferation, survival, and EMT; it is required for female reproductive function in mice, and its activity is regulated post-transcriptionally by miR-338-3p."},"narrative":{"mechanistic_narrative":"UBE2Q1 is an E2 ubiquitin-conjugating enzyme that controls the abundance of substrate proteins to drive cell proliferation, survival, and tumorigenic signaling [PMID:25987028, PMID:29027712]. Through its UBC domain it physically binds p53 and promotes p53 turnover, such that UBE2Q1 overexpression lowers p53 levels while its knockdown raises p53 and sensitizes cells to apoptotic signaling via bax, p21, and caspase-3 [PMID:25987028, PMID:24166684, PMID:37198983]. Beyond p53, UBE2Q1 stabilizes β-catenin to activate HIF-1α-driven hypoxic glycolysis (Warburg effect) and engages the β-catenin–EGFR–PI3K–Akt–mTOR axis, thereby promoting proliferation, S-phase entry, migration/invasion through EMT, and in vivo tumorigenicity in hepatocellular and colorectal cancer models [PMID:29027712, PMID:27602158, PMID:35156520]. It also interacts with DDX3 and regulates its ubiquitination in CML cells, where pharmacologic depletion of UBE2Q1 triggers mitochondrial apoptosis [PMID:39454411]. UBE2Q1 expression is held in check post-transcriptionally by miR-338-3p binding to its 3'-UTR [PMID:35156520, PMID:33770685]. Genetically, Ube2q1-knockout female mice display pleiotropic reproductive defects — altered oestrus, impaired embryo implantation, and increased embryonic lethality — establishing a required physiological role in female fertility [PMID:23108111]. Direct enzymatic demonstration of substrate ubiquitination by UBE2Q1 has not been reported in the available corpus; substrate degradation is inferred from gain/loss-of-function effects on protein abundance.","teleology":[{"year":2013,"claim":"Established that UBE2Q1 is genetically required for a physiological process, defining female fertility as an in vivo function rather than only a cancer-cell phenotype.","evidence":"Ube2q1 knockout mouse with multi-parameter reproductive phenotyping and uterine expression analysis","pmids":["23108111"],"confidence":"High","gaps":["The molecular substrate(s) mediating the reproductive defect are not identified","Does not connect the fertility phenotype to any specific ubiquitination event"]},{"year":2013,"claim":"Linked UBE2Q1 to p53 abundance in a neuronal context, showing bidirectional control (knockdown raises, overexpression lowers p53) with downstream apoptotic readouts.","evidence":"siRNA knockdown and overexpression in PC12 cells plus immunostaining in rat cortex","pmids":["24166684"],"confidence":"Medium","gaps":["No direct ubiquitination assay demonstrating UBE2Q1 conjugates ubiquitin to p53","Nuclear localization shown but not functionally tied to p53 regulation"]},{"year":2015,"claim":"Provided direct binding evidence that UBE2Q1 physically associates with p53, supporting a substrate relationship underlying p53 destabilization.","evidence":"Co-IP and GST pull-down with overexpression in MDA-MB-468 breast cancer cells","pmids":["25987028"],"confidence":"Medium","gaps":["Degradation mechanism inferred from protein levels, not shown by a ubiquitination assay","Single lab, single tumor type"]},{"year":2016,"claim":"Demonstrated a direct cell-cycle role: UBE2Q1 gain-of-function pushes cells from G0/G1 into S phase and increases proliferation and motility.","evidence":"Stable overexpression in SW1116 colorectal cells with MTT, colony, flow cytometry, and wound-healing assays","pmids":["27602158"],"confidence":"Medium","gaps":["Does not identify the substrate driving cell-cycle progression","Correlative pathway link not established here"]},{"year":2017,"claim":"Connected UBE2Q1 to oncogenic signaling, showing loss-of-function reduces proliferation/invasion and tumorigenicity through the β-catenin–EGFR–PI3K–Akt–mTOR axis.","evidence":"siRNA knockdown with in vitro phenotyping, orthotopic xenografts, and pathway Western blots in HCC lines","pmids":["29027712"],"confidence":"Medium","gaps":["Mechanism by which UBE2Q1 engages the β-catenin axis not defined","GADD45α induction mechanism unresolved"]},{"year":2021,"claim":"Identified the upstream regulatory input controlling UBE2Q1, establishing miR-338-3p as a direct 3'-UTR-targeting repressor with functional consequences for autophagy.","evidence":"Luciferase 3'-UTR reporter, overexpression rescue, and in vivo AR rat model in nasal epithelial cells","pmids":["33770685"],"confidence":"Medium","gaps":["Does not address ubiquitination substrates downstream of UBE2Q1","Effect mediated via AKT/mTOR but proximal target unknown"]},{"year":2022,"claim":"Defined a metabolic output: UBE2Q1 stabilizes β-catenin to activate HIF-1α and hypoxic glycolysis, situating it downstream of miR-338-3p in colorectal cancer.","evidence":"Knockdown/overexpression, glycolysis assays under hypoxia, Western blots, and in vivo tumor model","pmids":["35156520"],"confidence":"Medium","gaps":["β-catenin stabilization inferred from protein levels without direct ubiquitination assay","Whether UBE2Q1 acts directly on β-catenin or via an intermediate is unresolved"]},{"year":2023,"claim":"Mapped the structural basis of substrate recognition, localizing B4GALT1 and p53 binding to the UBC domain and identifying hot-spot regions.","evidence":"Co-IP with silver staining plus molecular docking of UBC domain against B4GALT1 and p53","pmids":["37198983"],"confidence":"Low","gaps":["Computational docking without functional ubiquitination validation","Single cell line; predicted interfaces not experimentally mutated"]},{"year":2024,"claim":"Expanded the substrate repertoire to DDX3 and showed UBE2Q1 is a druggable node, with bortezomib depleting it to trigger mitochondrial apoptosis in resistant CML cells.","evidence":"Co-IP of UBE2Q1–DDX3, ubiquitination and apoptosis readouts, and xenograft model in BCR::ABL T315I cells","pmids":["39454411"],"confidence":"Medium","gaps":["Whether bortezomib directly targets UBE2Q1 versus indirectly reducing its level is unclear","Direct E2 catalytic activity on DDX3 not reconstituted"]},{"year":null,"claim":"Whether UBE2Q1 directly catalyzes ubiquitin transfer to its named partners (p53, β-catenin, DDX3, B4GALT1) and which E3 ligases it pairs with remain unestablished.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No in vitro reconstituted ubiquitination assay for any proposed substrate","Cognate E3 ligase partner(s) unidentified","Substrate degradation throughout is inferred from steady-state protein levels"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,8]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,8]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[7]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[3]}],"complexes":[],"partners":["TP53","B4GALT1","DDX3X","CTNNB1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q7Z7E8","full_name":"Ubiquitin-conjugating enzyme E2 Q1","aliases":["E2 ubiquitin-conjugating enzyme Q1","Protein NICE-5","Ubiquitin carrier protein Q1","Ubiquitin-protein ligase Q1"],"length_aa":422,"mass_kda":46.1,"function":"Catalyzes the covalent attachment of ubiquitin to other proteins (PubMed:22496338). May be involved in hormonal homeostasis in females. Involved in regulation of B4GALT1 cell surface expression, B4GALT1-mediated cell adhesion to laminin and embryoid body formation (By similarity)","subcellular_location":"Nucleus; Cell projection, filopodium; Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/Q7Z7E8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBE2Q1","classification":"Not Classified","n_dependent_lines":227,"n_total_lines":1208,"dependency_fraction":0.1879139072847682},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/UBE2Q1","total_profiled":1310},"omim":[{"mim_id":"617429","title":"UBIQUITIN-CONJUGATING ENZYME E2 Q1; UBE2Q1","url":"https://www.omim.org/entry/617429"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Centrosome","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBE2Q1"},"hgnc":{"alias_symbol":["PRO3094","NICE-5"],"prev_symbol":["UBE2Q"]},"alphafold":{"accession":"Q7Z7E8","domains":[{"cath_id":"3.10.110.10","chopping":"36-77_98-171","consensus_level":"high","plddt":86.9327,"start":36,"end":171},{"cath_id":"3.10.110.10","chopping":"271-411","consensus_level":"high","plddt":93.5098,"start":271,"end":411}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z7E8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z7E8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z7E8-F1-predicted_aligned_error_v6.png","plddt_mean":78.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBE2Q1","jax_strain_url":"https://www.jax.org/strain/search?query=UBE2Q1"},"sequence":{"accession":"Q7Z7E8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q7Z7E8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q7Z7E8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z7E8"}},"corpus_meta":[{"pmid":"29027712","id":"PMC_29027712","title":"Upregulation of UBE2Q1 via gene copy number gain in hepatocellular carcinoma promotes cancer progression through β-catenin-EGFR-PI3K-Akt-mTOR signaling pathway.","date":"2017","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/29027712","citation_count":32,"is_preprint":false},{"pmid":"28592717","id":"PMC_28592717","title":"Hypomethylated Ubiquitin-Conjugating Enzyme2 Q1 (UBE2Q1) Gene Promoter in the Serum Is a Promising Biomarker for Hepatitis B Virus-Associated Hepatocellular Carcinoma.","date":"2017","source":"The Tohoku journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28592717","citation_count":26,"is_preprint":false},{"pmid":"24197692","id":"PMC_24197692","title":"UBE2Q1 expression in human colorectal tumors and cell lines.","date":"2013","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/24197692","citation_count":23,"is_preprint":false},{"pmid":"25987028","id":"PMC_25987028","title":"UBE2Q1 in a Human Breast Carcinoma Cell Line: Overexpression and Interaction with p53.","date":"2015","source":"Asian Pacific journal of cancer prevention : APJCP","url":"https://pubmed.ncbi.nlm.nih.gov/25987028","citation_count":20,"is_preprint":false},{"pmid":"24166684","id":"PMC_24166684","title":"Downregulation of UBE2Q1 is associated with neuronal apoptosis in rat brain cortex following traumatic brain injury.","date":"2013","source":"Journal of neuroscience research","url":"https://pubmed.ncbi.nlm.nih.gov/24166684","citation_count":20,"is_preprint":false},{"pmid":"22167327","id":"PMC_22167327","title":"Expression of the novel human gene, UBE2Q1, in breast tumors.","date":"2011","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/22167327","citation_count":19,"is_preprint":false},{"pmid":"32831649","id":"PMC_32831649","title":"FOXA1-induced circOSBPL10 potentiates cervical cancer cell proliferation and migration through miR-1179/UBE2Q1 axis.","date":"2020","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/32831649","citation_count":17,"is_preprint":false},{"pmid":"23108111","id":"PMC_23108111","title":"Embryo implantation failure and other reproductive defects in Ube2q1-deficient female mice.","date":"2013","source":"Reproduction (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/23108111","citation_count":17,"is_preprint":false},{"pmid":"35156520","id":"PMC_35156520","title":"LncRNA LINC00525 activates HIF-1α through miR-338-3p / UBE2Q1 / β-catenin axis to regulate the Warburg effect in colorectal cancer.","date":"2022","source":"Bioengineered","url":"https://pubmed.ncbi.nlm.nih.gov/35156520","citation_count":17,"is_preprint":false},{"pmid":"33770685","id":"PMC_33770685","title":"miR-338-3p inhibits autophagy in a rat model of allergic rhinitis after PM2.5 exposure through AKT/mTOR signaling by targeting UBE2Q1.","date":"2021","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/33770685","citation_count":15,"is_preprint":false},{"pmid":"26745068","id":"PMC_26745068","title":"Promoter Methylation Status of Two Novel Human Genes, UBE2Q1 and UBE2Q2, in Colorectal Cancer: a New Finding in Iranian Patients.","date":"2015","source":"Asian Pacific journal of cancer prevention : APJCP","url":"https://pubmed.ncbi.nlm.nih.gov/26745068","citation_count":14,"is_preprint":false},{"pmid":"27602158","id":"PMC_27602158","title":"Induction of cell proliferation, clonogenicity and cell accumulation in S phase as a consequence of human UBE2Q1 overexpression.","date":"2016","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/27602158","citation_count":9,"is_preprint":false},{"pmid":"25035859","id":"PMC_25035859","title":"UBE2Q1, as a Down Regulated Gene in Pediatric Acute Lymphoblastic Leukemia.","date":"2014","source":"International journal of molecular and cellular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/25035859","citation_count":5,"is_preprint":false},{"pmid":"39454411","id":"PMC_39454411","title":"Bortezomib induces cell apoptosis and increases the efficacy of αPD-1 in BCR::ABL T315I mutation CML by targeting UBE2Q1.","date":"2024","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/39454411","citation_count":2,"is_preprint":false},{"pmid":"37198983","id":"PMC_37198983","title":"Analysis of the Interaction of UBE2Q1 with B4GALT1 and P53: Experimental and Molecular Modeling Study.","date":"2023","source":"Protein and peptide letters","url":"https://pubmed.ncbi.nlm.nih.gov/37198983","citation_count":1,"is_preprint":false},{"pmid":"39389359","id":"PMC_39389359","title":"UBE2Q1 as a novel cancer biomarker for lung adenocarcinoma.","date":"2024","source":"The American journal of the medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39389359","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10539,"output_tokens":2785,"usd":0.036696,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10073,"output_tokens":3252,"usd":0.065833,"stage2_stop_reason":"end_turn"},"total_usd":0.102529,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"UBE2Q1 physically interacts with p53 protein (demonstrated by co-immunoprecipitation and GST pull-down in MDA-MB-468 breast cancer cells), and overexpression of UBE2Q1 reduces p53 protein levels, consistent with UBE2Q1-mediated ubiquitination and proteasomal degradation of p53.\",\n      \"method\": \"Co-immunoprecipitation, GST pull-down, Western blot after overexpression\",\n      \"journal\": \"Asian Pacific journal of cancer prevention : APJCP\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal in vivo and in vitro binding assays (Co-IP and GST pull-down), single lab, two orthogonal binding methods; degradation mechanism inferred but not directly demonstrated with ubiquitination assay\",\n      \"pmids\": [\"25987028\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"UBE2Q1 knockdown in PC12 neuronal cells increases p53 protein levels, while UBE2Q1 overexpression reduces p53 levels, linking UBE2Q1 to regulation of p53 abundance and downstream apoptotic signaling (increased bax, p21, active caspase-3 upon TBI-associated downregulation of UBE2Q1).\",\n      \"method\": \"siRNA knockdown and overexpression in PC12 cells, Western blot for p53/bax/p21/caspase-3, immunohistochemistry and immunofluorescence in rat brain cortex\",\n      \"journal\": \"Journal of neuroscience research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function and gain-of-function with defined molecular readout (p53 levels), single lab, two complementary approaches (KD and OE)\",\n      \"pmids\": [\"24166684\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"UBE2Q1 protein is expressed predominantly in the nucleus of neurons (with minority expression in astrocytes) in normal rat brain cortex, as established by double-immunofluorescence staining.\",\n      \"method\": \"Double-immunofluorescence staining in rat brain cortex\",\n      \"journal\": \"Journal of neuroscience research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single localization experiment in one tissue, single lab, no functional consequence directly tied to nuclear localization\",\n      \"pmids\": [\"24166684\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Mouse Ube2q1 knockout females exhibit pleiotropic reproductive defects including altered oestrus cycle, abnormal sexual behaviour, reduced offspring care, increased embryonic lethality, and decreased embryo implantation capacity, establishing a required role for UBE2Q1 in female fertility. Expression is induced in the uterus during pregnancy.\",\n      \"method\": \"Knockout mouse model (gene targeting), reproductive phenotype analysis, expression analysis by in situ hybridization/RT-PCR\",\n      \"journal\": \"Reproduction (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO mouse with defined multi-parameter reproductive phenotype; uterine expression verified by expression analysis; multiple orthogonal phenotypic readouts in a single rigorous study\",\n      \"pmids\": [\"23108111\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"UBE2Q1 is implicated in regulation of membrane B4GALT1 (beta-1,4-galactosyltransferase 1) protein, based on prior work cited in the Ube2q1 knockout paper.\",\n      \"method\": \"Referenced as prior finding in knockout paper (no direct experimental detail provided in this abstract)\",\n      \"journal\": \"Reproduction (Cambridge, England)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — referenced as an established finding without experimental detail provided in the abstract; cannot evaluate methodology\",\n      \"pmids\": [\"23108111\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Molecular docking and co-immunoprecipitation in stably transfected SW1116 colorectal cancer cells indicate that the UBC domain of UBE2Q1 has high binding affinity for B4GALT1 and p53 (both tetramerization and DNA-binding domains), identifying hot-spot interaction regions.\",\n      \"method\": \"Co-immunoprecipitation with silver staining, molecular docking (MOE software) of UBC domain (PDB: 2QGX) against B4GALT1 (2AGD) and p53 (1AIE, 1GZH)\",\n      \"journal\": \"Protein and peptide letters\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-IP in a single cell line and computational docking without functional ubiquitination assay validation; single lab\",\n      \"pmids\": [\"37198983\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"UBE2Q1 knockdown in HCC cell lines reduces cell proliferation, promotes apoptosis via induction of GADD45α, suppresses cell migration and invasion through regulation of EMT, and suppresses orthotopic tumorigenicity in vivo. UBE2Q1 activity is linked to the β-catenin-EGFR-PI3K-Akt-mTOR signaling pathway.\",\n      \"method\": \"siRNA knockdown, in vitro proliferation/apoptosis/migration/invasion assays, in vivo orthotopic xenograft model, Western blot for pathway components\",\n      \"journal\": \"Molecular carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with multiple phenotypic readouts in vitro and in vivo, pathway Western blot, single lab\",\n      \"pmids\": [\"29027712\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Stable overexpression of UBE2Q1 in SW1116 colorectal cancer cells increases cell proliferation, colony formation, motility, and causes a decrease in G0/G1 phase accumulation (shift toward S phase), demonstrating a direct role of UBE2Q1 in cell cycle progression.\",\n      \"method\": \"Stable transfection with pCMV6-AN-GFP-UBE2Q1, MTT assay, crystal violet colony assay, flow cytometry cell cycle analysis, wound healing assay\",\n      \"journal\": \"Oncology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gain-of-function with multiple orthogonal cellular assays, single lab\",\n      \"pmids\": [\"27602158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"UBE2Q1 interacts with DDX3 in BCR::ABL T315I mutation CML cells and regulates DDX3 ubiquitination; Bortezomib targets UBE2Q1 and reduces its protein level, leading to apoptosis via ROS production, mitochondrial membrane potential collapse, and cytochrome C release.\",\n      \"method\": \"Co-immunoprecipitation (UBE2Q1-DDX3 interaction), Western blot, cell viability assays, flow cytometry for ROS/mitochondrial potential, in vivo xenograft model\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP demonstrating UBE2Q1-DDX3 interaction with ubiquitination regulation, in vitro and in vivo functional data, single lab\",\n      \"pmids\": [\"39454411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"UBE2Q1 stabilizes β-catenin protein, which in turn activates HIF-1α to enhance hypoxia-driven glycolysis (Warburg effect) in colorectal cancer cells; this pathway is downstream of miR-338-3p targeting of UBE2Q1.\",\n      \"method\": \"siRNA knockdown and overexpression, luciferase reporter (for miR-338-3p/UBE2Q1 axis), Western blot for β-catenin and HIF-1α, glycolysis assays in hypoxia, in vivo tumor model\",\n      \"journal\": \"Bioengineered\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional rescue experiments with multiple readouts, in vitro and in vivo, single lab; β-catenin stabilization by UBE2Q1 inferred from OE/KD without direct ubiquitination assay\",\n      \"pmids\": [\"35156520\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"miR-338-3p directly targets the 3'-UTR of UBE2Q1 mRNA (luciferase reporter assay), negatively regulating its expression; overexpression of UBE2Q1 rescues miR-338-3p-mediated inhibition of autophagy via the AKT/mTOR pathway in nasal epithelial cells exposed to PM2.5.\",\n      \"method\": \"Luciferase reporter assay (miR-338-3p binding to UBE2Q1 3'-UTR), Western blot, overexpression rescue experiments, in vivo AR rat model\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct 3'-UTR reporter validation plus functional rescue, in vitro and in vivo, single lab\",\n      \"pmids\": [\"33770685\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBE2Q1 is a E2 ubiquitin-conjugating enzyme (containing a UBC domain and RWD domain) that physically interacts with and promotes ubiquitination/degradation of p53 and interacts with B4GALT1 and DDX3; it stabilizes β-catenin to activate HIF-1α-driven glycolysis and regulates the β-catenin-EGFR-PI3K-Akt-mTOR signaling axis, promoting cell cycle progression (S-phase entry), proliferation, survival, and EMT; it is required for female reproductive function in mice, and its activity is regulated post-transcriptionally by miR-338-3p.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBE2Q1 is an E2 ubiquitin-conjugating enzyme that controls the abundance of substrate proteins to drive cell proliferation, survival, and tumorigenic signaling [#0, #6]. Through its UBC domain it physically binds p53 and promotes p53 turnover, such that UBE2Q1 overexpression lowers p53 levels while its knockdown raises p53 and sensitizes cells to apoptotic signaling via bax, p21, and caspase-3 [#0, #1, #5]. Beyond p53, UBE2Q1 stabilizes \\u03b2-catenin to activate HIF-1\\u03b1-driven hypoxic glycolysis (Warburg effect) and engages the \\u03b2-catenin\\u2013EGFR\\u2013PI3K\\u2013Akt\\u2013mTOR axis, thereby promoting proliferation, S-phase entry, migration/invasion through EMT, and in vivo tumorigenicity in hepatocellular and colorectal cancer models [#6, #7, #9]. It also interacts with DDX3 and regulates its ubiquitination in CML cells, where pharmacologic depletion of UBE2Q1 triggers mitochondrial apoptosis [#8]. UBE2Q1 expression is held in check post-transcriptionally by miR-338-3p binding to its 3'-UTR [#9, #10]. Genetically, Ube2q1-knockout female mice display pleiotropic reproductive defects \\u2014 altered oestrus, impaired embryo implantation, and increased embryonic lethality \\u2014 establishing a required physiological role in female fertility [#3]. Direct enzymatic demonstration of substrate ubiquitination by UBE2Q1 has not been reported in the available corpus; substrate degradation is inferred from gain/loss-of-function effects on protein abundance.\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established that UBE2Q1 is genetically required for a physiological process, defining female fertility as an in vivo function rather than only a cancer-cell phenotype.\",\n      \"evidence\": \"Ube2q1 knockout mouse with multi-parameter reproductive phenotyping and uterine expression analysis\",\n      \"pmids\": [\"23108111\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The molecular substrate(s) mediating the reproductive defect are not identified\", \"Does not connect the fertility phenotype to any specific ubiquitination event\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Linked UBE2Q1 to p53 abundance in a neuronal context, showing bidirectional control (knockdown raises, overexpression lowers p53) with downstream apoptotic readouts.\",\n      \"evidence\": \"siRNA knockdown and overexpression in PC12 cells plus immunostaining in rat cortex\",\n      \"pmids\": [\"24166684\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct ubiquitination assay demonstrating UBE2Q1 conjugates ubiquitin to p53\", \"Nuclear localization shown but not functionally tied to p53 regulation\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided direct binding evidence that UBE2Q1 physically associates with p53, supporting a substrate relationship underlying p53 destabilization.\",\n      \"evidence\": \"Co-IP and GST pull-down with overexpression in MDA-MB-468 breast cancer cells\",\n      \"pmids\": [\"25987028\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Degradation mechanism inferred from protein levels, not shown by a ubiquitination assay\", \"Single lab, single tumor type\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Demonstrated a direct cell-cycle role: UBE2Q1 gain-of-function pushes cells from G0/G1 into S phase and increases proliferation and motility.\",\n      \"evidence\": \"Stable overexpression in SW1116 colorectal cells with MTT, colony, flow cytometry, and wound-healing assays\",\n      \"pmids\": [\"27602158\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not identify the substrate driving cell-cycle progression\", \"Correlative pathway link not established here\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected UBE2Q1 to oncogenic signaling, showing loss-of-function reduces proliferation/invasion and tumorigenicity through the \\u03b2-catenin\\u2013EGFR\\u2013PI3K\\u2013Akt\\u2013mTOR axis.\",\n      \"evidence\": \"siRNA knockdown with in vitro phenotyping, orthotopic xenografts, and pathway Western blots in HCC lines\",\n      \"pmids\": [\"29027712\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which UBE2Q1 engages the \\u03b2-catenin axis not defined\", \"GADD45\\u03b1 induction mechanism unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified the upstream regulatory input controlling UBE2Q1, establishing miR-338-3p as a direct 3'-UTR-targeting repressor with functional consequences for autophagy.\",\n      \"evidence\": \"Luciferase 3'-UTR reporter, overexpression rescue, and in vivo AR rat model in nasal epithelial cells\",\n      \"pmids\": [\"33770685\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not address ubiquitination substrates downstream of UBE2Q1\", \"Effect mediated via AKT/mTOR but proximal target unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined a metabolic output: UBE2Q1 stabilizes \\u03b2-catenin to activate HIF-1\\u03b1 and hypoxic glycolysis, situating it downstream of miR-338-3p in colorectal cancer.\",\n      \"evidence\": \"Knockdown/overexpression, glycolysis assays under hypoxia, Western blots, and in vivo tumor model\",\n      \"pmids\": [\"35156520\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"\\u03b2-catenin stabilization inferred from protein levels without direct ubiquitination assay\", \"Whether UBE2Q1 acts directly on \\u03b2-catenin or via an intermediate is unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mapped the structural basis of substrate recognition, localizing B4GALT1 and p53 binding to the UBC domain and identifying hot-spot regions.\",\n      \"evidence\": \"Co-IP with silver staining plus molecular docking of UBC domain against B4GALT1 and p53\",\n      \"pmids\": [\"37198983\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Computational docking without functional ubiquitination validation\", \"Single cell line; predicted interfaces not experimentally mutated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Expanded the substrate repertoire to DDX3 and showed UBE2Q1 is a druggable node, with bortezomib depleting it to trigger mitochondrial apoptosis in resistant CML cells.\",\n      \"evidence\": \"Co-IP of UBE2Q1\\u2013DDX3, ubiquitination and apoptosis readouts, and xenograft model in BCR::ABL T315I cells\",\n      \"pmids\": [\"39454411\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether bortezomib directly targets UBE2Q1 versus indirectly reducing its level is unclear\", \"Direct E2 catalytic activity on DDX3 not reconstituted\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether UBE2Q1 directly catalyzes ubiquitin transfer to its named partners (p53, \\u03b2-catenin, DDX3, B4GALT1) and which E3 ligases it pairs with remain unestablished.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro reconstituted ubiquitination assay for any proposed substrate\", \"Cognate E3 ligase partner(s) unidentified\", \"Substrate degradation throughout is inferred from steady-state protein levels\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 8]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TP53\", \"B4GALT1\", \"DDX3X\", \"CTNNB1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}