{"gene":"OTUB2","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2018,"finding":"OTUB2 deubiquitinates and stabilizes YAP and TAZ, activating them independently of the Hippo pathway. OTUB2 is poly-SUMOylated on lysine 233, and this SUMOylation enables it to bind YAP/TAZ via a novel SUMO-interacting motif (SIM) in YAP/TAZ. EGF and oncogenic KRAS induce OTUB2 poly-SUMOylation to activate YAP/TAZ.","method":"Gain-of-function cancer metastasis screen, co-immunoprecipitation, mutagenesis, SUMOylation assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (screen, Co-IP, mutagenesis, SUMOylation assays) in a single rigorous study identifying both the modification and the binding mechanism","pmids":["30472188"],"is_preprint":false},{"year":2009,"finding":"OTUB2 interacts with TRAF3 and TRAF6 (E3 ubiquitin ligases required for IRF3 and NF-κB activation, respectively) and mediates their deubiquitination, thereby negatively regulating virus-triggered type I IFN induction. Overexpression inhibited IRF3 and NF-κB activation; knockdown had the opposite effect.","method":"Co-immunoprecipitation, overexpression/knockdown with reporter assays for IRF3, NF-κB, and IFNB1","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP plus functional gain/loss-of-function with defined molecular readouts, replicated across TRAF3 and TRAF6","pmids":["19996094"],"is_preprint":false},{"year":2014,"finding":"OTUB2 suppresses RNF8-mediated L3MBTL1 ubiquitination and K63-linked ubiquitin chain formation at DNA double-strand breaks in a deubiquitinating-activity-dependent manner, thereby fine-tuning the speed of DSB-induced ubiquitination and promoting homologous recombination over NHEJ by limiting 53BP1/RAP80 accumulation and DSB-end protection.","method":"Depletion of OTUB2 (siRNA/shRNA), deubiquitination activity-dead mutants, immunofluorescence of DSB foci (53BP1, RAP80), ubiquitination assays, DNA repair pathway assays (HR vs. NHEJ reporters)","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — catalytic mutant analysis, in vitro/in vivo ubiquitination assays, and multiple orthogonal repair pathway readouts in a single rigorous study","pmids":["24560272"],"is_preprint":false},{"year":2019,"finding":"OTUB2 directly binds and deubiquitinates U2AF2 (a splicing factor), stabilizing it against proteasomal degradation, and thereby promotes the Warburg effect and AKT/mTOR pathway activation in non-small cell lung cancer.","method":"Co-immunoprecipitation, mass spectrometry, ubiquitination assays, knockdown/overexpression with glycolysis readouts and AKT/mTOR pathway markers","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus MS to identify interaction, followed by functional deubiquitination assays, single lab","pmids":["30662561"],"is_preprint":false},{"year":2021,"finding":"OTUB2 directly interacts with PKM2 and inhibits its ubiquitination by blocking the interaction between PKM2 and its E3 ligase Parkin, thereby enhancing PKM2 activity and promoting aerobic glycolysis in colorectal cancer.","method":"Co-immunoprecipitation, ubiquitination assays, glycolysis metabolic readouts, OTUB2 knockout in vivo","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ubiquitination assays with mechanistic epistasis (Parkin-PKM2 interaction disruption), single lab","pmids":["34671086"],"is_preprint":false},{"year":2024,"finding":"OTUB2 directly interacts with PD-L1 in the endoplasmic reticulum and removes ubiquitin modifications that would otherwise target PD-L1 for degradation, thereby stabilizing PD-L1 on the tumor cell surface and promoting immune evasion. A small-molecule inhibitor of OTUB2's deubiquitinase activity (without disrupting the OTUB2–PD-L1 interaction) reduces PD-L1 levels and suppresses tumor growth.","method":"Co-immunoprecipitation, genetic deletion of OTUB2 with flow cytometry for PD-L1, T cell cytotoxicity assays, pharmacological OTUB2 inhibitor in vivo","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, genetic KO, pharmacological inhibition, and functional T-cell killing assays with in vivo validation across multiple cancer types","pmids":["38167274"],"is_preprint":false},{"year":2018,"finding":"OTUB2 co-immunoprecipitates with the transcription factor Gli2, deubiquitinates it in vivo and in vitro (with catalytic mutants losing this activity), and stabilizes it against proteasomal degradation, thereby promoting Hedgehog signaling. Knockdown of OTUB2 suppresses osteogenic differentiation of MSCs.","method":"Co-immunoprecipitation, in vitro deubiquitination assay with OTUB2 catalytic mutants, cycloheximide chase, MG-132 rescue, osteogenesis assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro deubiquitination assay with mutagenesis confirmation, Co-IP, and functional cellular readout; single lab","pmids":["30241937"],"is_preprint":false},{"year":2020,"finding":"Molecular dynamics simulations revealed that OTUB2 possesses a catalytic triad characteristic of OTU cysteine proteases, but unlike OTUB1, its catalytic triad is disordered in the absence of ubiquitin and only rearranges to a catalytically competent state upon ubiquitin binding. His224 and Asn226 form a stable hydrogen bond in OTUB2. The active site is more solvent-accessible in OTUB2 than in OTUB1.","method":"Molecular dynamics simulations (computational; Tier 4)","journal":"The Journal of biological chemistry","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no experimental mutagenesis or structural validation reported in this abstract","pmids":["32265297"],"is_preprint":false},{"year":2022,"finding":"OTUB2 promotes deubiquitination and phosphorylation of STAT1, subsequently regulating CALML3 transcription. CALML3-mediated mitochondrial calcium signaling promotes oxidative phosphorylation and phosphatidylserine synthesis, and this OTUB2/STAT1/CALML3/PS axis exerts tumor-suppressive roles in tongue and esophageal SCC.","method":"Co-immunoprecipitation, ubiquitination assays, phosphorylation assays, transcriptional reporter assays, mouse models with orally administered phosphatidylserine","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus phosphorylation and ubiquitination assays with in vivo mouse model; single lab, multiple methods","pmids":["36288705"],"is_preprint":false},{"year":2024,"finding":"OTUB2 silencing in ovarian cancer destabilizes SNX29P2, which prevents HIF-1α from VHL-mediated degradation. Elevated HIF-1α then activates CA9 transcription, driving glycolysis, tumor progression, and chemoresistance.","method":"Genetic silencing of OTUB2, protein stability assays, HIF-1α/VHL interaction assays, CA9 transcriptional reporter, pharmacological CA9 inhibition with carboplatin synergy in vivo","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (protein stability, transcriptional assays, in vivo pharmacology), single lab","pmids":["38701117"],"is_preprint":false},{"year":2022,"finding":"OTUB2 stabilizes KRT80 by removing K48- and K63-linked ubiquitin chains, protecting it from proteasomal degradation. OTUB2 and KRT80 together activate AKT signaling to promote gastric cancer cell proliferation.","method":"Co-immunoprecipitation, ubiquitination assays specifying K48 and K63 linkages, knockdown/rescue experiments, in vivo xenograft","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — linkage-specific ubiquitination assays with Co-IP and in vivo validation; single lab","pmids":["35110531"],"is_preprint":false},{"year":2022,"finding":"OTUB2 binds to β-Catenin, deubiquitinates it (catalytically inactive OTUB2 fails to do so), stabilizes it, and enhances β-Catenin/TCF-mediated transcription including CCND1 and MYC in colorectal cancer cells.","method":"LC-MS/MS interactomics, reciprocal Co-immunoprecipitation, ubiquitination assays with catalytic mutant, cycloheximide chase, TCF-luciferase reporter","journal":"American journal of cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, catalytic mutant confirmation, and transcriptional readout; single lab, multiple orthogonal methods","pmids":["38058843"],"is_preprint":false},{"year":2022,"finding":"OTUB2 promotes CTNNB1 (β-Catenin) stability by interacting with E3 ligase TRAF6 and inhibiting lysosomal degradation of CTNNB1, which then upregulates ZEB1 to drive EMT and metastasis in intrahepatic cholangiocarcinoma.","method":"Co-immunoprecipitation, ubiquitination assays, lysosomal inhibitor experiments, knockdown/overexpression with EMT markers","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus mechanistic epistasis (TRAF6–CTNNB1–ZEB1 axis), single lab","pmids":["36858343"],"is_preprint":false},{"year":2025,"finding":"OTUB2 removes K48-linked polyubiquitin chains from RIPK3 via its active-site residue C51, inhibiting proteasomal degradation of RIPK3 and potentiating RIPK3-mediated neuronal necroptosis after ischemic stroke. Genetic deletion or pharmacological inhibition of OTUB2 reduced infarction and neurological deficits.","method":"OTUB2 knockout mice, active-site mutant (C51) analysis, K48-linkage-specific ubiquitination assays, pharmacological inhibitor in mouse stroke model and human brain organoids","journal":"EMBO molecular medicine","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — active-site mutagenesis, K48-specific ubiquitination assays, and in vivo genetic/pharmacological validation with functional phenotypic readouts","pmids":["40021931"],"is_preprint":false},{"year":2024,"finding":"OTUB2 deubiquitinates RIPK2, removing K48-linked polyubiquitin chains via its C51 active-site residue, thereby inhibiting proteasomal degradation of RIPK2 and promoting NOD2 signaling in macrophages. OTUB2-deficient mice show impaired cytokine/chemokine production in response to NOD2 agonist MDP and exacerbated colitis.","method":"Otub2 knockout mice, bone marrow transplantation, Co-IP, K48-specific ubiquitination assays, active-site mutant C51, cytokine assays","journal":"Clinical and translational medicine","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — active-site mutagenesis, K48-specific ubiquitination assays, genetic KO with in vivo colitis model and bone marrow chimeras, multiple orthogonal methods","pmids":["39358938"],"is_preprint":false},{"year":2025,"finding":"OTUB2 binds YAP and removes its K48-linked polyubiquitin chains, inhibiting YAP proteasomal degradation, thereby activating YAP-PFKFB3 transcriptional signaling and promoting vascular smooth muscle cell calcification in CKD. The YAP/TEAD1 complex binds the PFKFB3 promoter (confirmed by CUT&RUN-qPCR).","method":"Co-immunoprecipitation, K48-specific ubiquitination assays, AAV9-mediated VSMC-specific OTUB2 KO/overexpression in mice, CUT&RUN-qPCR, Von Kossa/Alizarin red staining","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, linkage-specific ubiquitination assays, in vivo VSMC-specific model; single lab","pmids":["39776804"],"is_preprint":false},{"year":2021,"finding":"OTUB2 promotes gastric cancer stemness by deubiquitinating and stabilizing KDM1A (LSD1), a histone demethylase. KDM1A overexpression reversed the effects of OTUB2 knockdown on stem cell markers and tumorigenicity. (NOTE: The original paper PMID:34646768 was retracted per PMID:37287909.)","method":"Co-immunoprecipitation, ubiquitination assays, sphere-formation assays, in vivo xenograft (RETRACTED)","journal":"Frontiers in oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Co-IP plus rescue experiment; paper has been formally retracted","pmids":["34646768"],"is_preprint":false},{"year":2025,"finding":"OTUB2 stabilizes TRAF6 by deubiquitinating it, leading to AKT pathway activation and promotion of TNBC cell proliferation and migration.","method":"Co-immunoprecipitation, ubiquitination assays, Western blotting, knockdown/overexpression functional assays","journal":"Oncology research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Co-IP and ubiquitination assays without catalytic mutant confirmation or in vivo validation reported","pmids":["40296903"],"is_preprint":false},{"year":2022,"finding":"OTUB2 acts as a deubiquitinase for SP1 protein, binding SP1 and inhibiting its K48-linked ubiquitination, thereby stabilizing SP1. SP1 then acts as a transcription factor for GINS1 (binding the 1822–1830 region of the GINS1 promoter), upregulating GINS1 to drive stemness, chemoresistance, and EMT in colon cancer.","method":"Co-immunoprecipitation, K48-specific ubiquitination assays, ChIP-qPCR, dual luciferase reporter, sphere-formation assays","journal":"Cell communication and signaling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, linkage-specific ubiquitination, ChIP-qPCR, luciferase reporter); single lab","pmids":["39210373"],"is_preprint":false},{"year":2022,"finding":"OTUB2 deubiquitinates and stabilizes PJA1 (an E3 ubiquitin ligase) in hepatocellular carcinoma cells, as shown by Co-IP and cycloheximide chase assays, and this stabilization promotes malignant proliferation and migration.","method":"Co-immunoprecipitation, cycloheximide chase, ubiquitination assays, knockdown/rescue experiments","journal":"Cellular and molecular bioengineering","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and CHX chase, single lab, no catalytic mutant confirmation","pmids":["35611163"],"is_preprint":false},{"year":2018,"finding":"OTUB2 acts as a direct downstream target of miR-29a-3p in papillary thyroid carcinoma. OTUB2 overexpression activates NF-κB signaling predominantly by stabilizing TRAF6 (confirmed by Western blot and luciferase reporter).","method":"Luciferase reporter assay for miR-29a-3p targeting of OTUB2, Western blot for TRAF6 stabilization, NF-κB reporter","journal":"Cancer management and research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — luciferase reporter and Western blot only; no direct deubiquitination assay for TRAF6 reported","pmids":["30588107"],"is_preprint":false},{"year":2025,"finding":"OTUB2 interacts with UBE2S (ubiquitin-conjugating enzyme E2S) and PGAM1; this complex inhibits K48-linked polyubiquitination-mediated degradation of PGAM1, increasing PGAM1 levels and promoting DNA repair, thereby reducing sensitivity of glioblastoma cells to temozolomide.","method":"Co-immunoprecipitation with mass spectrometry, ubiquitination assays (K48-linked), knockdown functional assays, in vivo GBM mouse model","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP/MS to identify complex, K48-specific ubiquitination assays, in vivo validation; single lab","pmids":["39904430"],"is_preprint":false},{"year":2025,"finding":"OTUB2 deubiquitinates NR4A1, suppressing its proteasomal degradation, with the C51 residue being essential for OTUB2 catalytic activity. This stabilization of NR4A1 suppresses macrophage M1 polarization and experimental preeclampsia in rodents.","method":"Co-immunoprecipitation, ubiquitination assays, OTUB2 C51 active-site mutant, gain/loss-of-function in macrophages, LPS-induced rat preeclampsia model","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — active-site mutant (C51) confirmation, Co-IP, ubiquitination assay, in vivo model; single lab","pmids":["40883596"],"is_preprint":false},{"year":2026,"finding":"OTUB2 stabilizes ALYREF (m5C reader) by removing K48-linked polyubiquitin chains, leading to increased ALYREF that enhances ABCG4 mRNA stability and expression, promoting ATP-dependent efflux of docetaxel in castration-resistant prostate cancer.","method":"Co-immunoprecipitation, K48-specific ubiquitination assays, mRNA stability assays, OTUB2 inhibitor (OTUB2-IN-1) treatment","journal":"International journal of biological sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and ubiquitination assays, single lab, no structural or reconstitution validation","pmids":["42003916"],"is_preprint":false},{"year":2026,"finding":"OTUB2 binds and deubiquitinates HASPIN kinase, counteracting K48-linked polyubiquitination and proteasomal degradation of HASPIN. KAT5-mediated acetylation of HASPIN at K751 enhances HASPIN's affinity for OTUB2, further promoting HASPIN stability and breast cancer cell proliferation/invasion.","method":"Co-immunoprecipitation, K48-specific ubiquitination assays, acetylation assays, OTUB2 knockdown/overexpression, in vivo xenograft","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, linkage-specific ubiquitination assay, acetylation-OTUB2 binding crosstalk, in vivo validation; single lab","pmids":["41896530"],"is_preprint":false},{"year":2026,"finding":"OTUB2 deubiquitinates and stabilizes EIF4A3; EIF4A3 in turn interacts with TPI1 to stabilize its mRNA, promoting glycolysis and TNBC progression.","method":"Co-immunoprecipitation, ubiquitination assays, mRNA stability assays, knockdown/overexpression functional assays, in vivo xenograft","journal":"Breast cancer research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and ubiquitination assays, single lab, no catalytic mutant validation reported","pmids":["41857621"],"is_preprint":false},{"year":2026,"finding":"OTUB2 deubiquitinates YAP and TAZ in gastric cancer cells, preventing their degradation, and activates TGF-β1/SMAD signaling (by inhibiting SMAD7) to promote M2 tumor-associated macrophage polarization. OTUB2 also stabilizes PD-L1 (CD274) via deubiquitination, enhancing immune evasion.","method":"Co-immunoprecipitation, Western blotting, ubiquitination assays, flow cytometry (M2 TAMs, CD274), T cell killing assays, in vivo tumor models","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus ubiquitination assays with functional immune readouts and in vivo validation; single lab","pmids":["41986305"],"is_preprint":false},{"year":2026,"finding":"OTUB2 interacts with voltage-gated potassium channel subunit Kv9.3, Peg3, and Camk2d in pancreatic β-cells (identified by Co-IP/mass spectrometry). OTUB2 inhibits NF-κB activity and enhances glucose-stimulated insulin secretion; OTUB2 KO mice exhibit impaired glucose tolerance and downregulation of K+ transporter genes.","method":"Co-immunoprecipitation with mass spectrometry, RNA sequencing of KO pancreata, glucose tolerance tests, MIN6 cell overexpression/silencing, AAV9-mediated overexpression in mouse pancreata","journal":"Frontiers in bioscience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP/MS for binding partners, in vivo KO and overexpression models with metabolic readouts, multiple orthogonal methods; single lab","pmids":["41914276"],"is_preprint":false},{"year":2025,"finding":"OTUB2 upregulates total and GTP-bound (active) Rac1 and activates the downstream MEK/ERK pathway, promoting pathological cardiac hypertrophy. Pharmacological inhibition of Rac1 with NSC23766 abolished OTUB2-mediated hypertrophic responses.","method":"AAV9-mediated cardiomyocyte-specific overexpression, TAC mouse model, Rac1 activity assay (GTP-bound Rac1 pulldown), pharmacological Rac1 inhibition, neonatal rat cardiomyocyte knockdown/overexpression","journal":"Human cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo cardiac-specific overexpression, Rac1 activation assay with pharmacological rescue; single lab","pmids":["41329260"],"is_preprint":false}],"current_model":"OTUB2 is an OTU-family cysteine deubiquitinase (active site C51) that removes ubiquitin chains—predominantly K48-linked—from a diverse set of substrates including YAP/TAZ, TRAF3, TRAF6, RIPK2, RIPK3, PKM2, PD-L1, U2AF2, Gli2, KRT80, β-Catenin, STAT1, SP1, KDM1A, HASPIN, EIF4A3, ALYREF, NR4A1, and others; it is itself regulated by poly-SUMOylation (K233), which enables substrate recognition via a novel SIM interaction with YAP/TAZ and is induced by EGF and oncogenic KRAS. Through substrate stabilization, OTUB2 modulates Hippo/YAP-TAZ, NF-κB, Hedgehog, NOD2-RIPK2, AKT/mTOR, and Warburg-effect pathways in contexts ranging from antiviral immunity, DNA double-strand break repair pathway choice, neuronal necroptosis, intestinal inflammation, and vascular calcification to tumor immune evasion via PD-L1 and pancreatic β-cell function."},"narrative":{"mechanistic_narrative":"OTUB2 is an OTU-family cysteine deubiquitinase that controls the abundance and signaling output of diverse substrates by trimming polyubiquitin chains—predominantly K48-linked—and thereby protecting target proteins from proteasomal degradation [PMID:24560272, PMID:40021931, PMID:39358938]. Its catalytic cysteine C51 is required for activity, and removal of K48 chains rather than chain processing per se underlies most of its documented stabilizing functions [PMID:40021931, PMID:39358938]. A defining regulatory layer is its own poly-SUMOylation on lysine 233, which is induced by EGF and oncogenic KRAS and enables OTUB2 to recognize substrates such as YAP/TAZ through a SUMO-interacting motif, deubiquitinating and stabilizing them to activate Hippo/YAP-TAZ transcriptional output independently of canonical Hippo regulation [PMID:30472188]. Through substrate stabilization OTUB2 acts as a node across multiple pathways: it deubiquitinates the E3 ligases TRAF3 and TRAF6 to negatively regulate virus-triggered type I interferon and NF-κB induction [PMID:19996094], stabilizes RIPK2 to promote NOD2 signaling in macrophages and intestinal inflammation [PMID:39358938], stabilizes RIPK3 to potentiate neuronal necroptosis after ischemic stroke [PMID:40021931], and stabilizes β-Catenin to enhance Wnt/TCF transcriptional programs [PMID:38058843]. In tumor settings OTUB2 drives glycolytic and Warburg-effect metabolism by stabilizing or activating substrates including U2AF2, PKM2, and SP1 [PMID:30662561, PMID:34671086, PMID:39210373], and promotes immune evasion by stabilizing PD-L1 in the endoplasmic reticulum, an activity that is druggable with a deubiquitinase inhibitor that lowers PD-L1 and suppresses tumor growth [PMID:38167274]. Beyond signaling, OTUB2 fine-tunes the DNA double-strand break response by suppressing RNF8-mediated K63 ubiquitination and limiting 53BP1/RAP80 accumulation, biasing repair toward homologous recombination [PMID:24560272]. No experimentally validated structural model exists; computational work indicates the OTU catalytic triad is disordered until ubiquitin binding triggers a productive rearrangement [PMID:32265297].","teleology":[{"year":2009,"claim":"Established the first cellular function of OTUB2 by showing it deubiquitinates the innate-immune E3 ligases TRAF3 and TRAF6 to restrain antiviral signaling.","evidence":"Reciprocal Co-IP plus overexpression/knockdown with IRF3, NF-κB, and IFNB1 reporter assays","pmids":["19996094"],"confidence":"High","gaps":["Ubiquitin chain linkage specificity on TRAF3/TRAF6 not defined","No catalytic mutant or in vivo model in this study"]},{"year":2014,"claim":"Placed OTUB2 in the DNA damage response, showing it tempers DSB-induced ubiquitination to influence repair pathway choice.","evidence":"Depletion, catalytically dead mutants, DSB focus imaging (53BP1, RAP80), and HR-vs-NHEJ reporter assays","pmids":["24560272"],"confidence":"High","gaps":["Direct K63 chain disassembly kinetics at chromatin not resolved","Recruitment mechanism to DSB sites unknown"]},{"year":2018,"claim":"Revealed OTUB2's own poly-SUMOylation (K233) as a switch that licenses substrate recognition, linking it to oncogenic Hippo/YAP-TAZ activation downstream of EGF/KRAS.","evidence":"Gain-of-function metastasis screen, Co-IP, SIM/SUMO mutagenesis, and SUMOylation assays in cancer cells","pmids":["30472188"],"confidence":"High","gaps":["SUMO E3 ligase responsible for OTUB2 modification not identified","Whether SIM-dependent recognition generalizes to non-YAP substrates untested"]},{"year":2018,"claim":"Extended OTUB2 substrate stabilization to Hedgehog signaling via Gli2 deubiquitination, connecting it to differentiation programs.","evidence":"Co-IP, in vitro deubiquitination with catalytic mutants, CHX chase, MG-132 rescue, osteogenesis assays","pmids":["30241937"],"confidence":"Medium","gaps":["Chain linkage on Gli2 not specified","Single-lab finding without in vivo validation"]},{"year":2019,"claim":"Identified a metabolic role through U2AF2 stabilization driving the Warburg effect and AKT/mTOR signaling in lung cancer.","evidence":"Co-IP/MS, ubiquitination assays, glycolysis and AKT/mTOR readouts","pmids":["30662561"],"confidence":"Medium","gaps":["Catalytic dependence not confirmed with active-site mutant","Single tumor context"]},{"year":2020,"claim":"Provided a structural rationale for OTUB2 catalysis, showing its OTU triad is disordered until ubiquitin binding induces a competent conformation.","evidence":"Molecular dynamics simulations comparing OTUB2 with OTUB1 (computational)","pmids":["32265297"],"confidence":"Low","gaps":["Computational prediction only; no experimental structure or mutagenesis validation","Functional consequence of substrate-induced ordering untested"]},{"year":2021,"claim":"Showed OTUB2 enhances glycolysis by shielding PKM2 from its E3 ligase Parkin, a non-canonical mechanism of blocking ubiquitination rather than removing chains.","evidence":"Co-IP, ubiquitination assays, glycolysis readouts, OTUB2 knockout in vivo in colorectal cancer","pmids":["34671086"],"confidence":"Medium","gaps":["Whether the effect requires OTUB2 catalytic activity vs steric blockade unclear","Single-lab context"]},{"year":2022,"claim":"Expanded the substrate repertoire to transcription and chromatin factors (β-Catenin, SP1, STAT1) coupling OTUB2 to Wnt, glycolytic, and tumor-suppressive transcriptional programs.","evidence":"Reciprocal Co-IP/LC-MS, K48-specific ubiquitination assays, catalytic mutants, ChIP-qPCR and luciferase reporters; in vivo models","pmids":["38058843","39210373","36288705","36858343"],"confidence":"Medium","gaps":["Context-dependent oncogenic vs tumor-suppressive roles not mechanistically reconciled","Substrate selectivity determinants undefined"]},{"year":2024,"claim":"Defined OTUB2 as a druggable stabilizer of PD-L1 in the ER, establishing a tumor-immune-evasion role and proof-of-concept pharmacology.","evidence":"Co-IP, genetic KO with PD-L1 flow cytometry, T-cell cytotoxicity, and a deubiquitinase inhibitor in vivo across cancer types","pmids":["38167274"],"confidence":"High","gaps":["PD-L1 ubiquitin linkage type not specified","Responsible E3 ligase for PD-L1 not identified"]},{"year":2024,"claim":"Demonstrated in vivo, active-site (C51)-dependent K48 deubiquitination of RIPK2, placing OTUB2 in NOD2 innate signaling and intestinal inflammation.","evidence":"Otub2 knockout mice, bone marrow chimeras, Co-IP, K48-specific ubiquitination assays, C51 mutant, cytokine and colitis readouts","pmids":["39358938"],"confidence":"High","gaps":["Whether SUMOylation gates RIPK2 recognition untested","Upstream control of OTUB2 in macrophages unknown"]},{"year":2025,"claim":"Showed C51-dependent K48 deubiquitination of RIPK3 drives neuronal necroptosis after stroke, identifying OTUB2 as a neuroprotective drug target.","evidence":"OTUB2 KO mice, C51 mutant, K48-specific ubiquitination assays, pharmacological inhibition in stroke model and human brain organoids","pmids":["40021931"],"confidence":"High","gaps":["Trigger for OTUB2 engagement of RIPK3 during ischemia undefined","Relationship to RIPK1/MLKL axis not detailed"]},{"year":2025,"claim":"Broadened the physiological reach of OTUB2 to vascular calcification, cardiac hypertrophy, and pancreatic β-cell function, including non-deubiquitinase outputs such as Rac1/MEK-ERK activation.","evidence":"AAV9 tissue-specific KO/overexpression, K48-specific ubiquitination assays, CUT&RUN-qPCR, Rac1 GTP pulldown with pharmacological rescue, Co-IP/MS in β-cells, glucose tolerance tests","pmids":["39776804","41329260","41914276"],"confidence":"Medium","gaps":["Direct substrate(s) for Rac1 activation not established","Mechanism linking OTUB2 to K+ channel subunits/insulin secretion unresolved"]},{"year":null,"claim":"How OTUB2 achieves substrate selectivity across its very broad target set, and whether SUMOylation-gated SIM recognition is a general versus YAP-specific mechanism, remains unresolved.","evidence":"No experimental structure of OTUB2 bound to substrate; selectivity determinants inferred only indirectly across single-substrate studies","pmids":[],"confidence":"Low","gaps":["No co-crystal/cryo-EM structure with ubiquitin or substrate","No systematic substrate-specificity or linkage-preference map","Rules governing oncogenic vs tumor-suppressive context unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,13,14]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[13,14,2]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,5]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[5]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,11,15]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[1,14,5]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[2]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[13,14]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[13]}],"complexes":[],"partners":["YAP1","WWTR1","TRAF3","TRAF6","RIPK2","RIPK3","CTNNB1","PD-L1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96DC9","full_name":"Ubiquitin thioesterase OTUB2","aliases":["Deubiquitinating enzyme OTUB2","OTU domain-containing ubiquitin aldehyde-binding protein 2","Otubain-2","Ubiquitin-specific-processing protease OTUB2"],"length_aa":234,"mass_kda":27.2,"function":"Hydrolase that can remove conjugated ubiquitin from proteins in vitro and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Mediates deubiquitination of 'Lys-11'-,'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, with a preference for 'Lys-63'-linked polyubiquitin chains","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q96DC9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/OTUB2","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/OTUB2","total_profiled":1310},"omim":[{"mim_id":"620790","title":"NEURODEVELOPMENTAL DISORDER WITH HYPOTONIA AND SEIZURES; NEDHS","url":"https://www.omim.org/entry/620790"},{"mim_id":"612024","title":"OTU DOMAIN-CONTAINING PROTEIN 7A; OTUD7A","url":"https://www.omim.org/entry/612024"},{"mim_id":"608338","title":"OTU DOMAIN-CONTAINING UBIQUITIN ALDEHYDE-BINDING PROTEIN 2; OTUB2","url":"https://www.omim.org/entry/608338"},{"mim_id":"105400","title":"AMYOTROPHIC LATERAL SCLEROSIS 1; ALS1","url":"https://www.omim.org/entry/105400"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"esophagus","ntpm":3.7},{"tissue":"skin 1","ntpm":7.2},{"tissue":"testis","ntpm":13.2}],"url":"https://www.proteinatlas.org/search/OTUB2"},"hgnc":{"alias_symbol":["FLJ21916","MGC3102"],"prev_symbol":["C14orf137"]},"alphafold":{"accession":"Q96DC9","domains":[{"cath_id":"1.20.1300.20","chopping":"47-191","consensus_level":"high","plddt":96.9226,"start":47,"end":191}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96DC9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96DC9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96DC9-F1-predicted_aligned_error_v6.png","plddt_mean":94.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=OTUB2","jax_strain_url":"https://www.jax.org/strain/search?query=OTUB2"},"sequence":{"accession":"Q96DC9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96DC9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96DC9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96DC9"}},"corpus_meta":[{"pmid":"30472188","id":"PMC_30472188","title":"OTUB2 Promotes Cancer Metastasis via Hippo-Independent Activation of YAP and TAZ.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30472188","citation_count":166,"is_preprint":false},{"pmid":"19996094","id":"PMC_19996094","title":"Regulation of virus-triggered signaling by OTUB1- and OTUB2-mediated deubiquitination of TRAF3 and TRAF6.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19996094","citation_count":161,"is_preprint":false},{"pmid":"30662561","id":"PMC_30662561","title":"OTUB2 stabilizes U2AF2 to promote the Warburg effect and tumorigenesis via the AKT/mTOR signaling pathway in non-small cell lung cancer.","date":"2019","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/30662561","citation_count":128,"is_preprint":false},{"pmid":"34671086","id":"PMC_34671086","title":"Deubiquitinase OTUB2 exacerbates the progression of colorectal cancer by promoting PKM2 activity and glycolysis.","date":"2021","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/34671086","citation_count":89,"is_preprint":false},{"pmid":"24560272","id":"PMC_24560272","title":"Fine-tuning of DNA damage-dependent ubiquitination by OTUB2 supports the DNA repair pathway choice.","date":"2014","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/24560272","citation_count":86,"is_preprint":false},{"pmid":"38167274","id":"PMC_38167274","title":"Pharmaceutical targeting of OTUB2 sensitizes tumors to cytotoxic T cells via degradation of PD-L1.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38167274","citation_count":52,"is_preprint":false},{"pmid":"30588107","id":"PMC_30588107","title":"miR-29a-3p inhibits growth, proliferation, and invasion of papillary thyroid carcinoma by suppressing NF-κB signaling via direct targeting of OTUB2.","date":"2018","source":"Cancer management and research","url":"https://pubmed.ncbi.nlm.nih.gov/30588107","citation_count":46,"is_preprint":false},{"pmid":"36288705","id":"PMC_36288705","title":"OTUB2 exerts tumor-suppressive roles via STAT1-mediated CALML3 activation and increased phosphatidylserine synthesis.","date":"2022","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36288705","citation_count":39,"is_preprint":false},{"pmid":"37334762","id":"PMC_37334762","title":"RBM15 m6 A modification-mediated OTUB2 upregulation promotes cervical cancer progression via the AKT/mTOR signaling.","date":"2023","source":"Environmental toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/37334762","citation_count":29,"is_preprint":false},{"pmid":"35110531","id":"PMC_35110531","title":"OTUB2 regulates KRT80 stability via deubiquitination and promotes tumour proliferation in gastric cancer.","date":"2022","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/35110531","citation_count":26,"is_preprint":false},{"pmid":"38701117","id":"PMC_38701117","title":"OTUB2 silencing promotes ovarian cancer via mitochondrial metabolic reprogramming and can be synthetically targeted by CA9 inhibition.","date":"2024","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/38701117","citation_count":25,"is_preprint":false},{"pmid":"32265297","id":"PMC_32265297","title":"Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32265297","citation_count":25,"is_preprint":false},{"pmid":"30241937","id":"PMC_30241937","title":"Regulation of Gli2 stability by deubiquitinase OTUB2.","date":"2018","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/30241937","citation_count":16,"is_preprint":false},{"pmid":"40021931","id":"PMC_40021931","title":"Deubiquitination of RIPK3 by OTUB2 potentiates neuronal necroptosis after ischemic stroke.","date":"2025","source":"EMBO molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40021931","citation_count":15,"is_preprint":false},{"pmid":"38480480","id":"PMC_38480480","title":"Honokiol induces ferroptosis in ovarian cancer cells through the regulation of YAP by OTUB2.","date":"2024","source":"The journal of obstetrics and gynaecology research","url":"https://pubmed.ncbi.nlm.nih.gov/38480480","citation_count":14,"is_preprint":false},{"pmid":"35850645","id":"PMC_35850645","title":"OTUB2 Regulates YAP1/TAZ to Promotes the Progression of Esophageal Squamous Cell Carcinoma.","date":"2022","source":"Biological procedures online","url":"https://pubmed.ncbi.nlm.nih.gov/35850645","citation_count":12,"is_preprint":false},{"pmid":"36316812","id":"PMC_36316812","title":"OTUB2 promotes the progression of endometrial cancer by regulating the PKM2-mediated PI3K/AKT signaling pathway.","date":"2022","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/36316812","citation_count":12,"is_preprint":false},{"pmid":"32830515","id":"PMC_32830515","title":"OTUB2 Promotes Homologous Recombination Repair Through Stimulating Rad51 Expression in Endometrial Cancer.","date":"2020","source":"Cell transplantation","url":"https://pubmed.ncbi.nlm.nih.gov/32830515","citation_count":11,"is_preprint":false},{"pmid":"35611163","id":"PMC_35611163","title":"OTUB2 Promotes Proliferation and Migration of Hepatocellular Carcinoma Cells by PJA1 Deubiquitylation.","date":"2022","source":"Cellular and molecular bioengineering","url":"https://pubmed.ncbi.nlm.nih.gov/35611163","citation_count":9,"is_preprint":false},{"pmid":"39776804","id":"PMC_39776804","title":"OTUB2 contributes to vascular calcification in chronic kidney disease via the YAP-mediated transcription of PFKFB3.","date":"2025","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/39776804","citation_count":8,"is_preprint":false},{"pmid":"39210373","id":"PMC_39210373","title":"OTU deubiquitinase, ubiquitin aldehyde binding 2  (OTUB2) modulates the stemness feature, chemoresistance, and epithelial-mesenchymal transition of colon cancer via regulating GINS complex subunit 1 (GINS1) expression.","date":"2024","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/39210373","citation_count":8,"is_preprint":false},{"pmid":"38058843","id":"PMC_38058843","title":"Inhibition of OTUB2 suppresses colorectal cancer cell growth by regulating β-Catenin signaling.","date":"2023","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/38058843","citation_count":8,"is_preprint":false},{"pmid":"34646768","id":"PMC_34646768","title":"OTUB2 Facilitates Tumorigenesis of Gastric Cancer Through Promoting KDM1A-Mediated Stem Cell-Like Properties.","date":"2021","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34646768","citation_count":8,"is_preprint":false},{"pmid":"35309903","id":"PMC_35309903","title":"The Emerging Role of OTUB2 in Diseases: From Cell Signaling Pathway to Physiological Function.","date":"2022","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/35309903","citation_count":7,"is_preprint":false},{"pmid":"36858343","id":"PMC_36858343","title":"Deubiquitinase OTUB2 promotes intrahepatic cholangiocarcinoma progression by stabilizing the CTNNB1-ZEB1 axis.","date":"2023","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/36858343","citation_count":6,"is_preprint":false},{"pmid":"39358938","id":"PMC_39358938","title":"Deubiquitination of RIPK2 by OTUB2 augments NOD2 signalling and protective effects in intestinal inflammation.","date":"2024","source":"Clinical and translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39358938","citation_count":6,"is_preprint":false},{"pmid":"40296903","id":"PMC_40296903","title":"OTUB2 promotes proliferation and metastasis of triple-negative breast cancer by deubiquitinating TRAF6.","date":"2025","source":"Oncology research","url":"https://pubmed.ncbi.nlm.nih.gov/40296903","citation_count":5,"is_preprint":false},{"pmid":"39904430","id":"PMC_39904430","title":"Ubiquitin-conjugating enzyme E2S decreases the sensitivity of glioblastoma cells to temozolomide by upregulating PGAM1 via the interaction with OTUB2.","date":"2025","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/39904430","citation_count":5,"is_preprint":false},{"pmid":"38819228","id":"PMC_38819228","title":"circRNA6448-14/miR-455-3p/OTUB2 axis stimulates glycolysis and stemness of esophageal squamous cell carcinoma.","date":"2024","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/38819228","citation_count":3,"is_preprint":false},{"pmid":"38702967","id":"PMC_38702967","title":"Exploring the regulatory role of FBXL19-AS1 in triple-negative breast cancer through the miR-378a-3p/OTUB2 axis.","date":"2024","source":"Cell biochemistry and function","url":"https://pubmed.ncbi.nlm.nih.gov/38702967","citation_count":3,"is_preprint":false},{"pmid":"38322554","id":"PMC_38322554","title":"The deubiquitinase OTUB2 promotes cervical cancer growth through stabilizing FOXM1.","date":"2024","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/38322554","citation_count":2,"is_preprint":false},{"pmid":"38909637","id":"PMC_38909637","title":"Grouper OTUB1 and OTUB2 promote red-spotted grouper nervous necrosis virus (RGNNV) replication by inhibiting the host innate immune response.","date":"2024","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/38909637","citation_count":2,"is_preprint":false},{"pmid":"40883596","id":"PMC_40883596","title":"OTUB2/NR4A1 restrains the development of preeclampsia by suppressing macrophage M1 polarization.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/40883596","citation_count":1,"is_preprint":false},{"pmid":"41914276","id":"PMC_41914276","title":"The Deubiquitinating Enzyme Otub2 Modulates Pancreatic Beta-Cells Function and Survival.","date":"2026","source":"Frontiers in bioscience (Landmark edition)","url":"https://pubmed.ncbi.nlm.nih.gov/41914276","citation_count":0,"is_preprint":false},{"pmid":"41857621","id":"PMC_41857621","title":"Deubiquitination and stabilization of EIF4A3 by OTUB2 contributes to TPI1-mediated glycolysis and TNBC progression.","date":"2026","source":"Breast cancer research : BCR","url":"https://pubmed.ncbi.nlm.nih.gov/41857621","citation_count":0,"is_preprint":false},{"pmid":"41329260","id":"PMC_41329260","title":"OTUB2 aggravates pathological cardiac hypertrophy through Rac1 activation.","date":"2025","source":"Human cell","url":"https://pubmed.ncbi.nlm.nih.gov/41329260","citation_count":0,"is_preprint":false},{"pmid":"41986305","id":"PMC_41986305","title":"OTUB2 induces M2 tumor-associated macrophage polarization and increases CD274 expression in gastric cancer cells to aggravate the progression of gastric cancer.","date":"2026","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/41986305","citation_count":0,"is_preprint":false},{"pmid":"41914283","id":"PMC_41914283","title":"OTUB2 Mutation Promotes Thyroid Collision Tumor's Insights From the Whole-exome Sequence.","date":"2026","source":"Frontiers in bioscience (Landmark edition)","url":"https://pubmed.ncbi.nlm.nih.gov/41914283","citation_count":0,"is_preprint":false},{"pmid":"42003916","id":"PMC_42003916","title":"OTUB2/ALYREF axis modulates the docetaxel resistance of castration-resistant prostate cancer via upregulating ABCG4-mediated drug efflux.","date":"2026","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/42003916","citation_count":0,"is_preprint":false},{"pmid":"42098079","id":"PMC_42098079","title":"OTUB2-mediated deubiquitination upregulates U2AF2 to promote colorectal cancer evasion of autophagy-ferroptosis.","date":"2026","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/42098079","citation_count":0,"is_preprint":false},{"pmid":"41896530","id":"PMC_41896530","title":"KAT5-mediated acetylation enhances the deubiquitination of HASPIN by OTUB2 and promotes breast cancer progression.","date":"2026","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/41896530","citation_count":0,"is_preprint":false},{"pmid":"42115880","id":"PMC_42115880","title":"Cancer-associated fibroblasts-derived exosomal circ_0067557 promotes colorectal cancer epithelial-mesenchymal transition via BHLHE40-mediated transcriptional activation of OTUB2.","date":"2026","source":"Biology direct","url":"https://pubmed.ncbi.nlm.nih.gov/42115880","citation_count":0,"is_preprint":false},{"pmid":"37287909","id":"PMC_37287909","title":"Retraction: OTUB2 facilitates tumorigenesis of gastric cancer through promoting KDM1A-mediated stem cell-like properties.","date":"2023","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/37287909","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":24413,"output_tokens":7376,"usd":0.091939,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":16542,"output_tokens":4347,"usd":0.095692,"stage2_stop_reason":"end_turn"},"total_usd":0.187631,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"OTUB2 deubiquitinates and stabilizes YAP and TAZ, activating them independently of the Hippo pathway. OTUB2 is poly-SUMOylated on lysine 233, and this SUMOylation enables it to bind YAP/TAZ via a novel SUMO-interacting motif (SIM) in YAP/TAZ. EGF and oncogenic KRAS induce OTUB2 poly-SUMOylation to activate YAP/TAZ.\",\n      \"method\": \"Gain-of-function cancer metastasis screen, co-immunoprecipitation, mutagenesis, SUMOylation assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (screen, Co-IP, mutagenesis, SUMOylation assays) in a single rigorous study identifying both the modification and the binding mechanism\",\n      \"pmids\": [\"30472188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"OTUB2 interacts with TRAF3 and TRAF6 (E3 ubiquitin ligases required for IRF3 and NF-κB activation, respectively) and mediates their deubiquitination, thereby negatively regulating virus-triggered type I IFN induction. Overexpression inhibited IRF3 and NF-κB activation; knockdown had the opposite effect.\",\n      \"method\": \"Co-immunoprecipitation, overexpression/knockdown with reporter assays for IRF3, NF-κB, and IFNB1\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP plus functional gain/loss-of-function with defined molecular readouts, replicated across TRAF3 and TRAF6\",\n      \"pmids\": [\"19996094\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"OTUB2 suppresses RNF8-mediated L3MBTL1 ubiquitination and K63-linked ubiquitin chain formation at DNA double-strand breaks in a deubiquitinating-activity-dependent manner, thereby fine-tuning the speed of DSB-induced ubiquitination and promoting homologous recombination over NHEJ by limiting 53BP1/RAP80 accumulation and DSB-end protection.\",\n      \"method\": \"Depletion of OTUB2 (siRNA/shRNA), deubiquitination activity-dead mutants, immunofluorescence of DSB foci (53BP1, RAP80), ubiquitination assays, DNA repair pathway assays (HR vs. NHEJ reporters)\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — catalytic mutant analysis, in vitro/in vivo ubiquitination assays, and multiple orthogonal repair pathway readouts in a single rigorous study\",\n      \"pmids\": [\"24560272\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"OTUB2 directly binds and deubiquitinates U2AF2 (a splicing factor), stabilizing it against proteasomal degradation, and thereby promotes the Warburg effect and AKT/mTOR pathway activation in non-small cell lung cancer.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, ubiquitination assays, knockdown/overexpression with glycolysis readouts and AKT/mTOR pathway markers\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus MS to identify interaction, followed by functional deubiquitination assays, single lab\",\n      \"pmids\": [\"30662561\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"OTUB2 directly interacts with PKM2 and inhibits its ubiquitination by blocking the interaction between PKM2 and its E3 ligase Parkin, thereby enhancing PKM2 activity and promoting aerobic glycolysis in colorectal cancer.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, glycolysis metabolic readouts, OTUB2 knockout in vivo\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ubiquitination assays with mechanistic epistasis (Parkin-PKM2 interaction disruption), single lab\",\n      \"pmids\": [\"34671086\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"OTUB2 directly interacts with PD-L1 in the endoplasmic reticulum and removes ubiquitin modifications that would otherwise target PD-L1 for degradation, thereby stabilizing PD-L1 on the tumor cell surface and promoting immune evasion. A small-molecule inhibitor of OTUB2's deubiquitinase activity (without disrupting the OTUB2–PD-L1 interaction) reduces PD-L1 levels and suppresses tumor growth.\",\n      \"method\": \"Co-immunoprecipitation, genetic deletion of OTUB2 with flow cytometry for PD-L1, T cell cytotoxicity assays, pharmacological OTUB2 inhibitor in vivo\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, genetic KO, pharmacological inhibition, and functional T-cell killing assays with in vivo validation across multiple cancer types\",\n      \"pmids\": [\"38167274\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"OTUB2 co-immunoprecipitates with the transcription factor Gli2, deubiquitinates it in vivo and in vitro (with catalytic mutants losing this activity), and stabilizes it against proteasomal degradation, thereby promoting Hedgehog signaling. Knockdown of OTUB2 suppresses osteogenic differentiation of MSCs.\",\n      \"method\": \"Co-immunoprecipitation, in vitro deubiquitination assay with OTUB2 catalytic mutants, cycloheximide chase, MG-132 rescue, osteogenesis assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro deubiquitination assay with mutagenesis confirmation, Co-IP, and functional cellular readout; single lab\",\n      \"pmids\": [\"30241937\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Molecular dynamics simulations revealed that OTUB2 possesses a catalytic triad characteristic of OTU cysteine proteases, but unlike OTUB1, its catalytic triad is disordered in the absence of ubiquitin and only rearranges to a catalytically competent state upon ubiquitin binding. His224 and Asn226 form a stable hydrogen bond in OTUB2. The active site is more solvent-accessible in OTUB2 than in OTUB1.\",\n      \"method\": \"Molecular dynamics simulations (computational; Tier 4)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no experimental mutagenesis or structural validation reported in this abstract\",\n      \"pmids\": [\"32265297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUB2 promotes deubiquitination and phosphorylation of STAT1, subsequently regulating CALML3 transcription. CALML3-mediated mitochondrial calcium signaling promotes oxidative phosphorylation and phosphatidylserine synthesis, and this OTUB2/STAT1/CALML3/PS axis exerts tumor-suppressive roles in tongue and esophageal SCC.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, phosphorylation assays, transcriptional reporter assays, mouse models with orally administered phosphatidylserine\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus phosphorylation and ubiquitination assays with in vivo mouse model; single lab, multiple methods\",\n      \"pmids\": [\"36288705\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"OTUB2 silencing in ovarian cancer destabilizes SNX29P2, which prevents HIF-1α from VHL-mediated degradation. Elevated HIF-1α then activates CA9 transcription, driving glycolysis, tumor progression, and chemoresistance.\",\n      \"method\": \"Genetic silencing of OTUB2, protein stability assays, HIF-1α/VHL interaction assays, CA9 transcriptional reporter, pharmacological CA9 inhibition with carboplatin synergy in vivo\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (protein stability, transcriptional assays, in vivo pharmacology), single lab\",\n      \"pmids\": [\"38701117\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUB2 stabilizes KRT80 by removing K48- and K63-linked ubiquitin chains, protecting it from proteasomal degradation. OTUB2 and KRT80 together activate AKT signaling to promote gastric cancer cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays specifying K48 and K63 linkages, knockdown/rescue experiments, in vivo xenograft\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — linkage-specific ubiquitination assays with Co-IP and in vivo validation; single lab\",\n      \"pmids\": [\"35110531\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUB2 binds to β-Catenin, deubiquitinates it (catalytically inactive OTUB2 fails to do so), stabilizes it, and enhances β-Catenin/TCF-mediated transcription including CCND1 and MYC in colorectal cancer cells.\",\n      \"method\": \"LC-MS/MS interactomics, reciprocal Co-immunoprecipitation, ubiquitination assays with catalytic mutant, cycloheximide chase, TCF-luciferase reporter\",\n      \"journal\": \"American journal of cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, catalytic mutant confirmation, and transcriptional readout; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"38058843\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUB2 promotes CTNNB1 (β-Catenin) stability by interacting with E3 ligase TRAF6 and inhibiting lysosomal degradation of CTNNB1, which then upregulates ZEB1 to drive EMT and metastasis in intrahepatic cholangiocarcinoma.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, lysosomal inhibitor experiments, knockdown/overexpression with EMT markers\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus mechanistic epistasis (TRAF6–CTNNB1–ZEB1 axis), single lab\",\n      \"pmids\": [\"36858343\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUB2 removes K48-linked polyubiquitin chains from RIPK3 via its active-site residue C51, inhibiting proteasomal degradation of RIPK3 and potentiating RIPK3-mediated neuronal necroptosis after ischemic stroke. Genetic deletion or pharmacological inhibition of OTUB2 reduced infarction and neurological deficits.\",\n      \"method\": \"OTUB2 knockout mice, active-site mutant (C51) analysis, K48-linkage-specific ubiquitination assays, pharmacological inhibitor in mouse stroke model and human brain organoids\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — active-site mutagenesis, K48-specific ubiquitination assays, and in vivo genetic/pharmacological validation with functional phenotypic readouts\",\n      \"pmids\": [\"40021931\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"OTUB2 deubiquitinates RIPK2, removing K48-linked polyubiquitin chains via its C51 active-site residue, thereby inhibiting proteasomal degradation of RIPK2 and promoting NOD2 signaling in macrophages. OTUB2-deficient mice show impaired cytokine/chemokine production in response to NOD2 agonist MDP and exacerbated colitis.\",\n      \"method\": \"Otub2 knockout mice, bone marrow transplantation, Co-IP, K48-specific ubiquitination assays, active-site mutant C51, cytokine assays\",\n      \"journal\": \"Clinical and translational medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — active-site mutagenesis, K48-specific ubiquitination assays, genetic KO with in vivo colitis model and bone marrow chimeras, multiple orthogonal methods\",\n      \"pmids\": [\"39358938\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUB2 binds YAP and removes its K48-linked polyubiquitin chains, inhibiting YAP proteasomal degradation, thereby activating YAP-PFKFB3 transcriptional signaling and promoting vascular smooth muscle cell calcification in CKD. The YAP/TEAD1 complex binds the PFKFB3 promoter (confirmed by CUT&RUN-qPCR).\",\n      \"method\": \"Co-immunoprecipitation, K48-specific ubiquitination assays, AAV9-mediated VSMC-specific OTUB2 KO/overexpression in mice, CUT&RUN-qPCR, Von Kossa/Alizarin red staining\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, linkage-specific ubiquitination assays, in vivo VSMC-specific model; single lab\",\n      \"pmids\": [\"39776804\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"OTUB2 promotes gastric cancer stemness by deubiquitinating and stabilizing KDM1A (LSD1), a histone demethylase. KDM1A overexpression reversed the effects of OTUB2 knockdown on stem cell markers and tumorigenicity. (NOTE: The original paper PMID:34646768 was retracted per PMID:37287909.)\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, sphere-formation assays, in vivo xenograft (RETRACTED)\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Co-IP plus rescue experiment; paper has been formally retracted\",\n      \"pmids\": [\"34646768\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUB2 stabilizes TRAF6 by deubiquitinating it, leading to AKT pathway activation and promotion of TNBC cell proliferation and migration.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, Western blotting, knockdown/overexpression functional assays\",\n      \"journal\": \"Oncology research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Co-IP and ubiquitination assays without catalytic mutant confirmation or in vivo validation reported\",\n      \"pmids\": [\"40296903\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUB2 acts as a deubiquitinase for SP1 protein, binding SP1 and inhibiting its K48-linked ubiquitination, thereby stabilizing SP1. SP1 then acts as a transcription factor for GINS1 (binding the 1822–1830 region of the GINS1 promoter), upregulating GINS1 to drive stemness, chemoresistance, and EMT in colon cancer.\",\n      \"method\": \"Co-immunoprecipitation, K48-specific ubiquitination assays, ChIP-qPCR, dual luciferase reporter, sphere-formation assays\",\n      \"journal\": \"Cell communication and signaling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, linkage-specific ubiquitination, ChIP-qPCR, luciferase reporter); single lab\",\n      \"pmids\": [\"39210373\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUB2 deubiquitinates and stabilizes PJA1 (an E3 ubiquitin ligase) in hepatocellular carcinoma cells, as shown by Co-IP and cycloheximide chase assays, and this stabilization promotes malignant proliferation and migration.\",\n      \"method\": \"Co-immunoprecipitation, cycloheximide chase, ubiquitination assays, knockdown/rescue experiments\",\n      \"journal\": \"Cellular and molecular bioengineering\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and CHX chase, single lab, no catalytic mutant confirmation\",\n      \"pmids\": [\"35611163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"OTUB2 acts as a direct downstream target of miR-29a-3p in papillary thyroid carcinoma. OTUB2 overexpression activates NF-κB signaling predominantly by stabilizing TRAF6 (confirmed by Western blot and luciferase reporter).\",\n      \"method\": \"Luciferase reporter assay for miR-29a-3p targeting of OTUB2, Western blot for TRAF6 stabilization, NF-κB reporter\",\n      \"journal\": \"Cancer management and research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — luciferase reporter and Western blot only; no direct deubiquitination assay for TRAF6 reported\",\n      \"pmids\": [\"30588107\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUB2 interacts with UBE2S (ubiquitin-conjugating enzyme E2S) and PGAM1; this complex inhibits K48-linked polyubiquitination-mediated degradation of PGAM1, increasing PGAM1 levels and promoting DNA repair, thereby reducing sensitivity of glioblastoma cells to temozolomide.\",\n      \"method\": \"Co-immunoprecipitation with mass spectrometry, ubiquitination assays (K48-linked), knockdown functional assays, in vivo GBM mouse model\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP/MS to identify complex, K48-specific ubiquitination assays, in vivo validation; single lab\",\n      \"pmids\": [\"39904430\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUB2 deubiquitinates NR4A1, suppressing its proteasomal degradation, with the C51 residue being essential for OTUB2 catalytic activity. This stabilization of NR4A1 suppresses macrophage M1 polarization and experimental preeclampsia in rodents.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, OTUB2 C51 active-site mutant, gain/loss-of-function in macrophages, LPS-induced rat preeclampsia model\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — active-site mutant (C51) confirmation, Co-IP, ubiquitination assay, in vivo model; single lab\",\n      \"pmids\": [\"40883596\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"OTUB2 stabilizes ALYREF (m5C reader) by removing K48-linked polyubiquitin chains, leading to increased ALYREF that enhances ABCG4 mRNA stability and expression, promoting ATP-dependent efflux of docetaxel in castration-resistant prostate cancer.\",\n      \"method\": \"Co-immunoprecipitation, K48-specific ubiquitination assays, mRNA stability assays, OTUB2 inhibitor (OTUB2-IN-1) treatment\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and ubiquitination assays, single lab, no structural or reconstitution validation\",\n      \"pmids\": [\"42003916\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"OTUB2 binds and deubiquitinates HASPIN kinase, counteracting K48-linked polyubiquitination and proteasomal degradation of HASPIN. KAT5-mediated acetylation of HASPIN at K751 enhances HASPIN's affinity for OTUB2, further promoting HASPIN stability and breast cancer cell proliferation/invasion.\",\n      \"method\": \"Co-immunoprecipitation, K48-specific ubiquitination assays, acetylation assays, OTUB2 knockdown/overexpression, in vivo xenograft\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, linkage-specific ubiquitination assay, acetylation-OTUB2 binding crosstalk, in vivo validation; single lab\",\n      \"pmids\": [\"41896530\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"OTUB2 deubiquitinates and stabilizes EIF4A3; EIF4A3 in turn interacts with TPI1 to stabilize its mRNA, promoting glycolysis and TNBC progression.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, mRNA stability assays, knockdown/overexpression functional assays, in vivo xenograft\",\n      \"journal\": \"Breast cancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and ubiquitination assays, single lab, no catalytic mutant validation reported\",\n      \"pmids\": [\"41857621\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"OTUB2 deubiquitinates YAP and TAZ in gastric cancer cells, preventing their degradation, and activates TGF-β1/SMAD signaling (by inhibiting SMAD7) to promote M2 tumor-associated macrophage polarization. OTUB2 also stabilizes PD-L1 (CD274) via deubiquitination, enhancing immune evasion.\",\n      \"method\": \"Co-immunoprecipitation, Western blotting, ubiquitination assays, flow cytometry (M2 TAMs, CD274), T cell killing assays, in vivo tumor models\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus ubiquitination assays with functional immune readouts and in vivo validation; single lab\",\n      \"pmids\": [\"41986305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"OTUB2 interacts with voltage-gated potassium channel subunit Kv9.3, Peg3, and Camk2d in pancreatic β-cells (identified by Co-IP/mass spectrometry). OTUB2 inhibits NF-κB activity and enhances glucose-stimulated insulin secretion; OTUB2 KO mice exhibit impaired glucose tolerance and downregulation of K+ transporter genes.\",\n      \"method\": \"Co-immunoprecipitation with mass spectrometry, RNA sequencing of KO pancreata, glucose tolerance tests, MIN6 cell overexpression/silencing, AAV9-mediated overexpression in mouse pancreata\",\n      \"journal\": \"Frontiers in bioscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP/MS for binding partners, in vivo KO and overexpression models with metabolic readouts, multiple orthogonal methods; single lab\",\n      \"pmids\": [\"41914276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUB2 upregulates total and GTP-bound (active) Rac1 and activates the downstream MEK/ERK pathway, promoting pathological cardiac hypertrophy. Pharmacological inhibition of Rac1 with NSC23766 abolished OTUB2-mediated hypertrophic responses.\",\n      \"method\": \"AAV9-mediated cardiomyocyte-specific overexpression, TAC mouse model, Rac1 activity assay (GTP-bound Rac1 pulldown), pharmacological Rac1 inhibition, neonatal rat cardiomyocyte knockdown/overexpression\",\n      \"journal\": \"Human cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo cardiac-specific overexpression, Rac1 activation assay with pharmacological rescue; single lab\",\n      \"pmids\": [\"41329260\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"OTUB2 is an OTU-family cysteine deubiquitinase (active site C51) that removes ubiquitin chains—predominantly K48-linked—from a diverse set of substrates including YAP/TAZ, TRAF3, TRAF6, RIPK2, RIPK3, PKM2, PD-L1, U2AF2, Gli2, KRT80, β-Catenin, STAT1, SP1, KDM1A, HASPIN, EIF4A3, ALYREF, NR4A1, and others; it is itself regulated by poly-SUMOylation (K233), which enables substrate recognition via a novel SIM interaction with YAP/TAZ and is induced by EGF and oncogenic KRAS. Through substrate stabilization, OTUB2 modulates Hippo/YAP-TAZ, NF-κB, Hedgehog, NOD2-RIPK2, AKT/mTOR, and Warburg-effect pathways in contexts ranging from antiviral immunity, DNA double-strand break repair pathway choice, neuronal necroptosis, intestinal inflammation, and vascular calcification to tumor immune evasion via PD-L1 and pancreatic β-cell function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"OTUB2 is an OTU-family cysteine deubiquitinase that controls the abundance and signaling output of diverse substrates by trimming polyubiquitin chains—predominantly K48-linked—and thereby protecting target proteins from proteasomal degradation [#2, #13, #14]. Its catalytic cysteine C51 is required for activity, and removal of K48 chains rather than chain processing per se underlies most of its documented stabilizing functions [#13, #14]. A defining regulatory layer is its own poly-SUMOylation on lysine 233, which is induced by EGF and oncogenic KRAS and enables OTUB2 to recognize substrates such as YAP/TAZ through a SUMO-interacting motif, deubiquitinating and stabilizing them to activate Hippo/YAP-TAZ transcriptional output independently of canonical Hippo regulation [#0]. Through substrate stabilization OTUB2 acts as a node across multiple pathways: it deubiquitinates the E3 ligases TRAF3 and TRAF6 to negatively regulate virus-triggered type I interferon and NF-\\u03baB induction [#1], stabilizes RIPK2 to promote NOD2 signaling in macrophages and intestinal inflammation [#14], stabilizes RIPK3 to potentiate neuronal necroptosis after ischemic stroke [#13], and stabilizes \\u03b2-Catenin to enhance Wnt/TCF transcriptional programs [#11]. In tumor settings OTUB2 drives glycolytic and Warburg-effect metabolism by stabilizing or activating substrates including U2AF2, PKM2, and SP1 [#3, #4, #18], and promotes immune evasion by stabilizing PD-L1 in the endoplasmic reticulum, an activity that is druggable with a deubiquitinase inhibitor that lowers PD-L1 and suppresses tumor growth [#5]. Beyond signaling, OTUB2 fine-tunes the DNA double-strand break response by suppressing RNF8-mediated K63 ubiquitination and limiting 53BP1/RAP80 accumulation, biasing repair toward homologous recombination [#2]. No experimentally validated structural model exists; computational work indicates the OTU catalytic triad is disordered until ubiquitin binding triggers a productive rearrangement [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established the first cellular function of OTUB2 by showing it deubiquitinates the innate-immune E3 ligases TRAF3 and TRAF6 to restrain antiviral signaling.\",\n      \"evidence\": \"Reciprocal Co-IP plus overexpression/knockdown with IRF3, NF-\\u03baB, and IFNB1 reporter assays\",\n      \"pmids\": [\"19996094\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin chain linkage specificity on TRAF3/TRAF6 not defined\", \"No catalytic mutant or in vivo model in this study\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Placed OTUB2 in the DNA damage response, showing it tempers DSB-induced ubiquitination to influence repair pathway choice.\",\n      \"evidence\": \"Depletion, catalytically dead mutants, DSB focus imaging (53BP1, RAP80), and HR-vs-NHEJ reporter assays\",\n      \"pmids\": [\"24560272\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct K63 chain disassembly kinetics at chromatin not resolved\", \"Recruitment mechanism to DSB sites unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed OTUB2's own poly-SUMOylation (K233) as a switch that licenses substrate recognition, linking it to oncogenic Hippo/YAP-TAZ activation downstream of EGF/KRAS.\",\n      \"evidence\": \"Gain-of-function metastasis screen, Co-IP, SIM/SUMO mutagenesis, and SUMOylation assays in cancer cells\",\n      \"pmids\": [\"30472188\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"SUMO E3 ligase responsible for OTUB2 modification not identified\", \"Whether SIM-dependent recognition generalizes to non-YAP substrates untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended OTUB2 substrate stabilization to Hedgehog signaling via Gli2 deubiquitination, connecting it to differentiation programs.\",\n      \"evidence\": \"Co-IP, in vitro deubiquitination with catalytic mutants, CHX chase, MG-132 rescue, osteogenesis assays\",\n      \"pmids\": [\"30241937\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Chain linkage on Gli2 not specified\", \"Single-lab finding without in vivo validation\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified a metabolic role through U2AF2 stabilization driving the Warburg effect and AKT/mTOR signaling in lung cancer.\",\n      \"evidence\": \"Co-IP/MS, ubiquitination assays, glycolysis and AKT/mTOR readouts\",\n      \"pmids\": [\"30662561\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Catalytic dependence not confirmed with active-site mutant\", \"Single tumor context\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Provided a structural rationale for OTUB2 catalysis, showing its OTU triad is disordered until ubiquitin binding induces a competent conformation.\",\n      \"evidence\": \"Molecular dynamics simulations comparing OTUB2 with OTUB1 (computational)\",\n      \"pmids\": [\"32265297\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Computational prediction only; no experimental structure or mutagenesis validation\", \"Functional consequence of substrate-induced ordering untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed OTUB2 enhances glycolysis by shielding PKM2 from its E3 ligase Parkin, a non-canonical mechanism of blocking ubiquitination rather than removing chains.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, glycolysis readouts, OTUB2 knockout in vivo in colorectal cancer\",\n      \"pmids\": [\"34671086\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the effect requires OTUB2 catalytic activity vs steric blockade unclear\", \"Single-lab context\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Expanded the substrate repertoire to transcription and chromatin factors (\\u03b2-Catenin, SP1, STAT1) coupling OTUB2 to Wnt, glycolytic, and tumor-suppressive transcriptional programs.\",\n      \"evidence\": \"Reciprocal Co-IP/LC-MS, K48-specific ubiquitination assays, catalytic mutants, ChIP-qPCR and luciferase reporters; in vivo models\",\n      \"pmids\": [\"38058843\", \"39210373\", \"36288705\", \"36858343\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Context-dependent oncogenic vs tumor-suppressive roles not mechanistically reconciled\", \"Substrate selectivity determinants undefined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined OTUB2 as a druggable stabilizer of PD-L1 in the ER, establishing a tumor-immune-evasion role and proof-of-concept pharmacology.\",\n      \"evidence\": \"Co-IP, genetic KO with PD-L1 flow cytometry, T-cell cytotoxicity, and a deubiquitinase inhibitor in vivo across cancer types\",\n      \"pmids\": [\"38167274\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"PD-L1 ubiquitin linkage type not specified\", \"Responsible E3 ligase for PD-L1 not identified\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated in vivo, active-site (C51)-dependent K48 deubiquitination of RIPK2, placing OTUB2 in NOD2 innate signaling and intestinal inflammation.\",\n      \"evidence\": \"Otub2 knockout mice, bone marrow chimeras, Co-IP, K48-specific ubiquitination assays, C51 mutant, cytokine and colitis readouts\",\n      \"pmids\": [\"39358938\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SUMOylation gates RIPK2 recognition untested\", \"Upstream control of OTUB2 in macrophages unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed C51-dependent K48 deubiquitination of RIPK3 drives neuronal necroptosis after stroke, identifying OTUB2 as a neuroprotective drug target.\",\n      \"evidence\": \"OTUB2 KO mice, C51 mutant, K48-specific ubiquitination assays, pharmacological inhibition in stroke model and human brain organoids\",\n      \"pmids\": [\"40021931\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Trigger for OTUB2 engagement of RIPK3 during ischemia undefined\", \"Relationship to RIPK1/MLKL axis not detailed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Broadened the physiological reach of OTUB2 to vascular calcification, cardiac hypertrophy, and pancreatic \\u03b2-cell function, including non-deubiquitinase outputs such as Rac1/MEK-ERK activation.\",\n      \"evidence\": \"AAV9 tissue-specific KO/overexpression, K48-specific ubiquitination assays, CUT&RUN-qPCR, Rac1 GTP pulldown with pharmacological rescue, Co-IP/MS in \\u03b2-cells, glucose tolerance tests\",\n      \"pmids\": [\"39776804\", \"41329260\", \"41914276\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct substrate(s) for Rac1 activation not established\", \"Mechanism linking OTUB2 to K+ channel subunits/insulin secretion unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How OTUB2 achieves substrate selectivity across its very broad target set, and whether SUMOylation-gated SIM recognition is a general versus YAP-specific mechanism, remains unresolved.\",\n      \"evidence\": \"No experimental structure of OTUB2 bound to substrate; selectivity determinants inferred only indirectly across single-substrate studies\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No co-crystal/cryo-EM structure with ubiquitin or substrate\", \"No systematic substrate-specificity or linkage-preference map\", \"Rules governing oncogenic vs tumor-suppressive context unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 13, 14]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [13, 14, 2]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 11, 15]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [1, 14, 5]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [13, 14]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"YAP1\", \"WWTR1\", \"TRAF3\", \"TRAF6\", \"RIPK2\", \"RIPK3\", \"CTNNB1\", \"PD-L1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}