{"gene":"OTUD3","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2015,"finding":"OTUD3 directly interacts with PTEN, de-polyubiquitylates it, and stabilizes PTEN protein levels. Depletion of OTUD3 leads to activation of Akt signaling and promotes cellular transformation. Loss-of-function OTUD3 mutations found in human cancers either abolish catalytic activity or attenuate interaction with PTEN.","method":"Co-immunoprecipitation, ubiquitination assay, OTUD3 transgenic mice, loss-of-function mutant analysis, in vitro deubiquitylation assay","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (Co-IP, in vitro DUB assay, transgenic mouse model, catalytic mutants) in a single rigorous study","pmids":["26280536"],"is_preprint":false},{"year":2019,"finding":"OTUD3 interacts with, deubiquitylates, and stabilizes GRP78 (glucose-regulated protein 78 kDa) in lung cancer cells, promoting lung tumorigenesis. In vivo deletion of OTUD3 slows KrasG12D-driven lung adenocarcinoma progression.","method":"Co-immunoprecipitation, ubiquitination assay, OTUD3 knockout mice with KrasG12D lung cancer model, knockdown/rescue experiments","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — reciprocal Co-IP, ubiquitination assay, and in vivo mouse genetic model with defined phenotypic readout","pmids":["31266968"],"is_preprint":false},{"year":2020,"finding":"OTUD3 directly hydrolyzes K63-linked polyubiquitination of MAVS to suppress innate antiviral immune signaling. The catalytic activity of OTUD3 is regulated by acetylation of Lys129; SIRT1 removes this acetylation upon virus infection, inactivating OTUD3 and permitting antiviral immunity.","method":"In vitro deubiquitylation assay, acetylation site mutagenesis (K129 mutants), OTUD3-deficient mice, SIRT1 knockdown/overexpression, viral infection models","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro DUB assay with linkage specificity, acetylation site mutagenesis, and in vivo mouse knockout model with orthogonal methods","pmids":["32679077"],"is_preprint":false},{"year":2020,"finding":"OTUD3 directly interacts with p53, deubiquitylates it, and protects p53 from MDM2-mediated ubiquitination and degradation. The catalytically inactive OTUD3 mutant fails to stabilize p53. The interaction occurs through the amino-terminal OTU region of OTUD3.","method":"Co-immunoprecipitation, GST pulldown, ubiquitination assay, half-life analysis, catalytic mutant (inactive mutant), proliferation and apoptosis assays","journal":"BMC cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and GST pulldown plus ubiquitination assay in single lab, multiple orthogonal methods","pmids":["32571254"],"is_preprint":false},{"year":2020,"finding":"CHIP (carboxyl terminus of Hsc70-interacting protein) is an E3 ubiquitin ligase for OTUD3; CHIP interacts with OTUD3, polyubiquitylates it, and promotes OTUD3 proteasomal degradation.","method":"Co-immunoprecipitation, ubiquitination assay, CHIP knockdown/overexpression, CHIP catalytic mutant analysis","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and ubiquitination assay in single lab with multiple methods","pmids":["32483383"],"is_preprint":false},{"year":2021,"finding":"OTUD3 directly interacts with ZFP36 and stabilizes it by inhibiting FBXW7-mediated K48-linked polyubiquitination. ZFP36 in turn binds VEGF-C 3'-UTR and recruits RNA degrading complex to promote VEGF-C mRNA decay.","method":"Co-immunoprecipitation, ubiquitination assay, RNA decay assay, ZFP36 rescue experiments, esophageal cancer cell and in vivo models","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, and functional mRNA decay readout in single lab","pmids":["34853315"],"is_preprint":false},{"year":2021,"finding":"OTUD3 directly binds ACTN4 (alpha-actinin 4) and deubiquitinates it to stabilize ACTN4 protein, driving hepatocellular carcinoma growth and metastasis.","method":"Mass spectrometry identification, Co-immunoprecipitation, ubiquitination assay, gain- and loss-of-function assays, xenograft mouse model","journal":"Aging","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS identification plus Co-IP and ubiquitination assay, single lab","pmids":["34380780"],"is_preprint":false},{"year":2022,"finding":"OTUD3 functions as a deubiquitylase for IRP2 (iron regulatory protein 2), interacting with IRP2 in the cytoplasm, removing polyubiquitin to stabilize IRP2 in an iron-independent manner. OTUD3 knockout mice display nigral iron accumulation, motor deficits, and nigrostriatal dopaminergic neurodegeneration resembling Parkinson's disease pathology.","method":"Co-immunoprecipitation, ubiquitination assay, OTUD3 knockout mouse model, neurochemical and behavioral analyses","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — Co-IP, ubiquitination assay, and in vivo knockout mouse model with defined neurodegeneration phenotype","pmids":["35490179"],"is_preprint":false},{"year":2022,"finding":"OTUD3 binds to RIG-I and MDA5, removing K63-linked ubiquitination to reduce their binding to viral RNA and the adaptor MAVS, suppressing RNA virus-triggered innate immunity. Simultaneously, OTUD3 associates with cGAS and removes K48-linked ubiquitination at Lys279, stabilizing cGAS and enhancing its DNA-binding ability, thus promoting DNA virus-triggered innate immunity.","method":"Co-immunoprecipitation, ubiquitination assay with linkage-specific analysis, Otud3-deficient mice and zebrafish, viral infection models (RNA and DNA viruses)","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple substrates identified with linkage-specific DUB activity, validated in both mouse and zebrafish in vivo models","pmids":["35675783"],"is_preprint":false},{"year":2022,"finding":"OTUD3 cleaves preferentially K6- and K63-linked polyubiquitin chains (not primarily degradative linkages). In cells, OTUD3 is present in the cytoplasm where it can bind to microtubules. In Xenopus embryos, Otud3 deficiency impairs cranial neural crest-derived structures and causes movement defects.","method":"In vitro deubiquitylation assay with linkage-specific ubiquitin chains, cellular fractionation/immunofluorescence for microtubule co-localization, Xenopus morpholino knockdown","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — in vitro DUB assay with linkage specificity and in vivo Xenopus model, single lab","pmids":["36503125"],"is_preprint":false},{"year":2022,"finding":"OTUD3 is regulated by glucose and fatty acid signals through CBP-dependent acetylation, which promotes OTUD3 nuclear translocation. In the nucleus, OTUD3 stabilizes PPARδ by deubiquitination, regulating genes involved in glucose and lipid metabolism and oxidative phosphorylation. A c.863G>A OTUD3 mutation reduces protein stability and catalytic activity and is found in a family with early-onset diabetes.","method":"Otud3-/- mouse model with high-fat diet, acetylation mutant analysis, nuclear fractionation/immunofluorescence, ubiquitination assay for PPARδ, PPARδ agonist rescue experiment","journal":"Cell metabolism","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vivo knockout mouse model, acetylation site mutagenesis, nuclear translocation assay, and substrate ubiquitination assay with pharmacological rescue","pmids":["35675826"],"is_preprint":false},{"year":2023,"finding":"OTUD3 is recruited to cytosolic cGAS-DNA complexes through its ability to directly bind DNA. In addition to stabilizing cGAS (removing ubiquitin to prevent degradation), OTUD3 enhances cGAS enzymatic activity, thereby promoting anti-DNA virus immune response.","method":"Proximity labeling (TurboID) of cGAS to identify interactors, Co-immunoprecipitation, in vitro DNA-binding assay, cGAS enzymatic activity assay, viral infection assay","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proximity labeling plus Co-IP and enzymatic activity assay, single lab with multiple orthogonal methods","pmids":["36966392"],"is_preprint":false},{"year":2023,"finding":"OTUD3 regulates the ubiquitination level of Fortilin through its OTU domain, stabilizing Fortilin, which in turn maintains Fortilin-IRE1α interaction. OTUD3 knockdown reduces Fortilin-IRE1α interaction, enhancing IRE1α activity and promoting ER stress-induced apoptosis of dopaminergic neurons.","method":"Co-immunoprecipitation, ubiquitination assay, OTUD3 knockout mouse histology, IRE1α inhibitor rescue (STF-083010), ER stress marker analysis (PDI, XBP1s)","journal":"Antioxidants (Basel, Switzerland)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ubiquitination assay with pharmacological rescue in single lab","pmids":["37107185"],"is_preprint":false},{"year":2024,"finding":"OTUD3 is a deubiquitylase of eIF2α (eukaryotic initiation factor 2α), removing K27-linked polyubiquitylation from eIF2α. This decreases interactions between eIF2α and the kinase EIF2AK3 (PERK), thereby antagonizing the integrated stress response (ISR) and suppressing liver cancer progression.","method":"Co-immunoprecipitation, ubiquitination assay with K27-linkage specificity, OTUD3 deficient mice with N-nitrosodiethylamine-induced HCC, ISRIB pharmacological rescue","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — linkage-specific ubiquitination assay, in vivo knockout mouse model of HCC, and pharmacological rescue with multiple orthogonal methods","pmids":["38996071"],"is_preprint":false},{"year":2024,"finding":"PLK1 mediates phosphorylation of OTUD3 at Ser326, which enhances OTUD3 binding to and deubiquitination of YY1 transcription factor, stabilizing YY1 and promoting colorectal cancer progression.","method":"Co-immunoprecipitation, ubiquitination assay, PLK1 kinase assay, phospho-site mutant analysis (S326), colorectal cancer cell proliferation assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, and phosphorylation site mutagenesis in single lab","pmids":["38351178"],"is_preprint":false},{"year":2024,"finding":"OTUD3 deubiquitinates SLC7A11, protecting it from proteasomal degradation, thereby promoting cystine transport, reducing intracellular ROS levels, and suppressing ferroptosis to drive sunitinib resistance in clear cell renal cell carcinoma.","method":"Co-immunoprecipitation, ubiquitination assay, ferroptosis assay (ROS levels), sunitinib resistance cell models and in vivo xenograft","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ubiquitination assay with functional ferroptosis readout, single lab","pmids":["40716486"],"is_preprint":false},{"year":2024,"finding":"OTUD3 deubiquitinates and stabilizes KPTN (kaptin), acting through its OTU domain. Ubiquitination of KPTN primarily occurs at lysine 49 and is a non-degradative functional modification. OTUD3 promotes GATOR1 lysosomal localization via KPTN, thereby suppressing mTORC1 signaling activation independent of PTEN.","method":"In vivo ubiquitination assay, Co-immunoprecipitation, CRISPR/Cas9 OTUD3 knockout, immunofluorescence for GATOR1 localization, NMR, mTORC1 signaling readout (S6K phosphorylation)","journal":"Frontiers in pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo ubiquitination assay, CRISPR knockout, and localization imaging in single lab","pmids":["38288086"],"is_preprint":false},{"year":2024,"finding":"OTUD3 deubiquitinates PLK1 via K48-linked ubiquitin chains, stabilizing PLK1 protein. Stabilized PLK1 activates the PI3K/AKT signaling pathway, reducing ferroptosis after cerebral ischemia-reperfusion injury. OTUD3 binds the amino acid sequence 35-305 of PLK1.","method":"Co-immunoprecipitation-mass spectrometry, ubiquitination assay (K48-linkage specific), OTUD3 overexpression/knockdown in OGD/R neuron model, PLK1 inhibitor rescue, in vivo cerebral I/R mouse model","journal":"Clinical and translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP-MS and ubiquitination assay with functional pathway readout, single lab","pmids":["40462502"],"is_preprint":false},{"year":2025,"finding":"OTUD3 deubiquitinates STING in intestinal fibroblasts to suppress pathological STING activation triggered by microbial cyclic GMP-AMP (cGAMP). Mice harboring a UC-risk missense variant in Otud3 show pathological features of ulcerative colitis after fecal microbiota transplantation from UC patients.","method":"OTUD3 knockout and missense variant knock-in mice, fecal microbiota transplantation, ubiquitination assay for STING, intestinal fibroblast functional assays","journal":"Science immunology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vivo mouse genetic models (KO and knock-in variant), ubiquitination assay, and functional microbiota transplant challenge","pmids":["40680146"],"is_preprint":false},{"year":2025,"finding":"GSK3β phosphorylates OTUD3 at Ser9, which enhances OTUD3 affinity for ARID3A and further stabilizes ARID3A by removing ubiquitin chains at K240 and K329 of ARID3A, promoting cholangiocarcinoma progression.","method":"Co-immunoprecipitation, ubiquitination assay, site-specific mutagenesis (K240/K329 of ARID3A, Ser9 of OTUD3), in vivo and in vitro CCA proliferation/metastasis assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay with site mutagenesis, single lab with multiple orthogonal methods","pmids":["40181152"],"is_preprint":false},{"year":2025,"finding":"The E3 ubiquitin ligase β-TRCP1 targets OTUD3 for ubiquitination and proteasomal degradation through RSK3-mediated phosphorylation of a conserved 'ESG' degron motif in OTUD3. Cytosolic DNA challenge inactivates the β-TRCP1/RSK3 pathway (via mTORC2 signaling, independently of canonical Ras/MEK/ERK and DNA damage kinases), resulting in OTUD3 stabilization and enhanced cGAS activation.","method":"Co-immunoprecipitation, ubiquitination assay, phospho-degron mutagenesis (ESG motif), RSK3 kinase assay, mTORC2 inhibitor experiments, viral/DNA challenge cell assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, mutagenesis of phospho-degron, and kinase/pathway inhibitor dissection in single lab","pmids":["41999888"],"is_preprint":false},{"year":2025,"finding":"OTUD3 deubiquitinates and stabilizes SMAD7, thereby inhibiting TGF-β signaling, suppressing EMT, and reducing breast cancer cell invasion. Catalytically inactive OTUD3 (C76 site mutant) fails to regulate BHLHE22 and SMAD7 protein stability.","method":"Co-immunoprecipitation, ubiquitination assay, catalytic mutant (C76), luciferase reporter assay for TGF-β pathway, transwell invasion assay, 3D matrigel culture","journal":"Cancer cell international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, and catalytic site mutagenesis with functional invasion readout, single lab","pmids":["40382618"],"is_preprint":false},{"year":2025,"finding":"OTUD3 deubiquitinates MYL12A and PD-L1 to enhance cell survival and immune evasion (CD8+ T cell exhaustion) in DLBCL. The OTUD3 inhibitor Rupatadine competitively binds OTUD3 and diminishes deubiquitination of both MYL12A and PD-L1.","method":"Co-immunoprecipitation, ubiquitination assay, competitive binding assay for Rupatadine-OTUD3, CD8+ T cell co-culture exhaustion assay","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ubiquitination assay with functional immune cell readout, single lab","pmids":["39097608"],"is_preprint":false},{"year":2025,"finding":"OTUD3 deubiquitinates and stabilizes PPARγ in retinal pigment epithelium cells, protecting against oxidative stress and inflammation in diabetic retinopathy.","method":"OTUD3 knockdown/knockout mouse model, ubiquitination assay for PPARγ, PPARγ agonist rescue, ROS/apoptosis assays in RPE cell lines","journal":"Life sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, PPARγ as substrate supported by knockdown and agonist rescue but limited direct ubiquitination mechanistic detail in abstract","pmids":["40886936"],"is_preprint":false},{"year":2026,"finding":"OTUD3 deubiquitinates and stabilizes BHLHE22 transcription factor in triple-negative breast cancer, suppressing tumor progression. The catalytic C76 mutant of OTUD3 fails to stabilize BHLHE22. BHLHE22 mediates the antitumor effect of OTUD3 by transcriptionally inhibiting CDT1.","method":"Co-immunoprecipitation, ubiquitination assay, catalytic site mutant (C76), dual luciferase reporter assay for CDT1 transcription, mRNA-seq, in vivo xenograft","journal":"Breast cancer research : BCR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ubiquitination assay with catalytic mutant and transcriptional readout, single lab","pmids":["41484895"],"is_preprint":false},{"year":2026,"finding":"Mitochondrial ECSIT promotes the localization of OTUD3 to mitochondria, where OTUD3 deubiquitinates SIRT3 to stabilize it, thereby inhibiting mtDNA oxidation and alleviating MASH-associated metabolic disorders.","method":"ECSIT mitochondria-targeted transgenic mice, OTUD3 mitochondrial fractionation/immunofluorescence, ubiquitination assay for SIRT3, HFHC and MCD diet MASH models","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo transgenic mouse model with fractionation and ubiquitination assay, single lab","pmids":["41640247"],"is_preprint":false},{"year":2026,"finding":"OTUD3 deubiquitinates and stabilizes TEX264, a receptor for ER-phagy. Stabilized TEX264 enables ER-phagy-mediated degradation of KDM5B in lung cancer cells treated with teniposide. OTUD3 silencing dampens teniposide-driven ER-phagy and KDM5B inhibition.","method":"Co-immunoprecipitation, ubiquitination assay, OTUD3 knockdown, ER-phagy flux assay, lung cancer organoid and xenograft models","journal":"European journal of pharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, and functional ER-phagy readout in single lab","pmids":["41763483"],"is_preprint":false}],"current_model":"OTUD3 is a cytoplasmic OTU-family deubiquitinase with a strong preference for K6, K27, K48, and K63-linked polyubiquitin chains that stabilizes a wide array of substrates (PTEN, GRP78, IRP2, p53, MAVS, cGAS, eIF2α, ACTN4, ZFP36, SMAD7, YY1, KPTN, PPARδ, SLC7A11, PLK1, TEX264, SIRT3, and others) by removing polyubiquitin to prevent proteasomal degradation; its catalytic activity is tightly regulated by reversible acetylation at Lys129 (controlled by CBP and SIRT1) and by phosphorylation-dependent degron recognition (RSK3/β-TRCP1 axis and PLK1/GSK3β-mediated priming), placing OTUD3 as a context-dependent hub that can suppress or promote tumorigenesis depending on which substrate dominates in a given tissue, and that controls innate antiviral/DNA-sensing immunity, iron homeostasis, integrated stress response, and metabolic regulation."},"narrative":{"mechanistic_narrative":"OTUD3 is an OTU-family deubiquitinase that removes polyubiquitin from a broad set of substrates to control their stability and activity, positioning it as a context-dependent regulator of tumorigenesis, innate immunity, and metabolism [PMID:26280536, PMID:32679077, PMID:35675826]. It hydrolyzes specific ubiquitin linkages—preferentially K6- and K63-linked chains in vitro—and resides largely in the cytoplasm, where it can associate with microtubules [PMID:36503125]. Its substrate scope spans tumor-suppressive targets such as PTEN, whose stabilization restrains Akt signaling and transformation [PMID:26280536], p53, which it protects from MDM2-mediated degradation [PMID:32571254], and SMAD7 [PMID:40382618], as well as pro-tumorigenic targets including GRP78 in lung cancer [PMID:31266968] and ACTN4 in hepatocellular carcinoma [PMID:34380780], explaining its dual roles across tissues. In innate immunity OTUD3 acts bidirectionally: it strips K63-linked ubiquitin from MAVS, RIG-I, and MDA5 to dampen RNA-virus signaling [PMID:32679077, PMID:35675783], while binding DNA and cGAS to remove K48-linked ubiquitin and enhance cGAS enzymatic activity, thereby promoting DNA-sensing immunity [PMID:35675783, PMID:36966392], and it restrains pathological STING activation in intestinal fibroblasts [PMID:40680146]. OTUD3 also stabilizes IRP2 to govern iron homeostasis, with its loss producing nigral iron accumulation and dopaminergic neurodegeneration [PMID:35490179], and antagonizes the integrated stress response by deubiquitinating eIF2α [PMID:38996071]. Its activity is tightly regulated by post-translational control: reversible Lys129 acetylation governs catalytic activity and CBP-driven nuclear translocation toward metabolic substrates such as PPARδ [PMID:32679077, PMID:35675826], CHIP and the RSK3/β-TRCP1 axis target it for degradation [PMID:32483383, PMID:41999888], and PLK1- and GSK3β-mediated phosphorylation redirect its substrate engagement [PMID:38351178, PMID:40181152]. An OTUD3 missense variant linked to early-onset diabetes reduces protein stability and catalytic activity [PMID:35675826], and a UC-risk variant predisposes mice to ulcerative colitis-like pathology [PMID:40680146].","teleology":[{"year":2015,"claim":"Established OTUD3 as a functional deubiquitinase with a defined substrate by showing it directly stabilizes PTEN to restrain Akt-driven transformation, framing OTUD3 as a tumor suppressor.","evidence":"Co-IP, in vitro DUB assay, transgenic mice, and cancer-associated loss-of-function mutants","pmids":["26280536"],"confidence":"High","gaps":["Linkage specificity on PTEN not defined","Whether PTEN is the dominant substrate in all tissues unresolved"]},{"year":2019,"claim":"Revealed that OTUD3 can also be pro-tumorigenic by stabilizing GRP78, showing its role is substrate- and tissue-context dependent rather than uniformly tumor-suppressive.","evidence":"Reciprocal Co-IP, ubiquitination assay, and OTUD3 knockout in a KrasG12D lung adenocarcinoma mouse model","pmids":["31266968"],"confidence":"High","gaps":["Mechanism reconciling opposing PTEN vs GRP78 roles not addressed","Ubiquitin linkage on GRP78 not specified"]},{"year":2020,"claim":"Identified acetylation at Lys129 as a switch controlling OTUD3 catalytic activity and connected OTUD3 to innate antiviral signaling via K63-linked deubiquitination of MAVS.","evidence":"In vitro DUB assay, K129 acetylation mutants, SIRT1 manipulation, and OTUD3-deficient mice with viral infection","pmids":["32679077"],"confidence":"High","gaps":["How acetylation alters catalytic geometry not structurally defined","CBP as the writer not established in this study"]},{"year":2020,"claim":"Extended the tumor-suppressor model by showing OTUD3 stabilizes p53 against MDM2, and identified CHIP as an E3 ligase that degrades OTUD3, defining its turnover control.","evidence":"Co-IP, GST pulldown, ubiquitination and half-life assays (p53); reciprocal Co-IP and ubiquitination with CHIP mutants","pmids":["32571254","32483383"],"confidence":"Medium","gaps":["Single-lab findings without in vivo confirmation","Linkage type of CHIP-mediated chains not specified"]},{"year":2022,"claim":"Defined OTUD3's intrinsic linkage preference (K6/K63), cytoplasmic/microtubule localization, and roles in iron homeostasis and DNA/RNA virus sensing, establishing the bidirectional immune function and a neurodegeneration phenotype.","evidence":"Linkage-specific in vitro DUB assays, fractionation/IF, IRP2 and RIG-I/MDA5/cGAS ubiquitination assays, OTUD3 knockout mice and zebrafish, Xenopus knockdown","pmids":["35490179","35675783","36503125"],"confidence":"High","gaps":["How a single DUB selects opposing immune substrates (RIG-I vs cGAS) mechanistically unclear","Microtubule binding functional consequence undefined"]},{"year":2022,"claim":"Showed acetylation directs OTUD3 to the nucleus to stabilize PPARδ for metabolic gene control, and linked an OTUD3 mutation to early-onset diabetes, broadening OTUD3 beyond cytoplasmic functions.","evidence":"Otud3-/- mice on high-fat diet, acetylation mutants, nuclear fractionation/IF, PPARδ ubiquitination assay with agonist rescue, human family mutation","pmids":["35675826"],"confidence":"High","gaps":["Acetyltransferase/deacetylase pairing for nuclear translocation incomplete","Causality of the c.863G>A variant at population scale not established"]},{"year":2023,"claim":"Mechanistically deepened the cGAS axis by demonstrating OTUD3 directly binds DNA to be recruited to cGAS-DNA complexes and enhances cGAS enzymatic activity beyond mere stabilization.","evidence":"TurboID proximity labeling, Co-IP, in vitro DNA-binding and cGAS activity assays, viral infection","pmids":["36966392"],"confidence":"Medium","gaps":["Structural basis of DNA binding not resolved","Single-lab enzymatic enhancement awaits independent confirmation"]},{"year":2024,"claim":"Diversified substrate repertoire and regulatory inputs: OTUD3 antagonizes the integrated stress response via K27-linked deubiquitination of eIF2α, and phosphorylation by PLK1 (Ser326) and stabilization of PLK1, KPTN, and SLC7A11 connect OTUD3 to mTORC1, ferroptosis, and cell-cycle control.","evidence":"Linkage-specific ubiquitination assays, knockout HCC mice with ISRIB rescue, kinase assays, phospho-site mutants, and functional ferroptosis/mTORC1 readouts","pmids":["38996071","38351178","38288086","40716486","40462502"],"confidence":"High","gaps":["Many substrate relationships rest on single-lab data","How phosphorylation reshapes substrate selection not generalized"]},{"year":2025,"claim":"Mapped degron-based turnover (RSK3/β-TRCP1 via an ESG motif), GSK3β priming for ARID3A engagement, and expanded immune/metabolic/cancer substrates (STING, SMAD7, PPARγ, MYL12A/PD-L1), reinforcing OTUD3 as a heavily PTM-gated hub with therapeutic targetability.","evidence":"Phospho-degron mutagenesis with mTORC2 inhibitors, site-specific ubiquitination assays, knock-in UC-variant mice with fecal transplant, catalytic-mutant invasion assays, and Rupatadine competitive-binding/T-cell exhaustion assays","pmids":["40680146","40181152","40382618","39097608","41999888","40886936"],"confidence":"Medium","gaps":["Disease-variant causality (UC) established only in mouse models","PPARγ substrate relationship is low-confidence with limited direct ubiquitination detail"]},{"year":2026,"claim":"Localized OTUD3 to additional compartments and pathways: ECSIT-dependent mitochondrial recruitment to stabilize SIRT3, and stabilization of BHLHE22 and the ER-phagy receptor TEX264, linking OTUD3 to mitochondrial protection, ER-phagy, and tumor suppression.","evidence":"Mitochondria-targeted transgenic mice with fractionation and SIRT3 ubiquitination assay; Co-IP, catalytic mutants, transcriptional and ER-phagy flux readouts in cancer models","pmids":["41640247","41484895","41763483"],"confidence":"Medium","gaps":["Mitochondrial vs nuclear vs cytoplasmic targeting determinants not unified","Single-lab substrate claims lacking cross-validation"]},{"year":null,"claim":"How OTUD3 selects among its many substrates and opposing roles in a given tissue—and whether a unifying structural or regulatory logic governs its linkage specificity and subcellular partitioning—remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model integrating PTM-driven substrate switching","No systematic comparison of which substrate dominates per tissue","Therapeutic window of OTUD3 inhibition across opposing functions undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3,7,8,13]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,2,9,13]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[11]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[7,9,11]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[10]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[9]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[25]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[2,8,11,18,22]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,1,6,7,13]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[7,10,25]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,2,13]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[13]}],"complexes":[],"partners":["PTEN","GRP78","MAVS","CGAS","IRP2","P53","CHIP","PPARD"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5T2D3","full_name":"OTU domain-containing protein 3","aliases":[],"length_aa":398,"mass_kda":45.1,"function":"Deubiquitinating enzyme that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. Also hydrolyzes heterotypic (mixed and branched) and homotypic chains (PubMed:23827681, PubMed:32011234, PubMed:35675826). Important regulator of energy metabolism (PubMed:35675826). Glucose and fatty acids trigger its nuclear translocation by CBP-dependent acetylation (PubMed:35675826). In the nucleus, deubiquitinates and stabilizes the nuclear receptor PPARD regulating the expression of various genes involved in glucose and lipid metabolism and oxidative phosphorylation (PubMed:35675826). Also acts as a negative regulator of the ribosome quality control (RQC) by mediating deubiquitination of 40S ribosomal proteins RPS10/eS10 and RPS20/uS10, thereby antagonizing ZNF598-mediated 40S ubiquitination (PubMed:32011234)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q5T2D3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/OTUD3","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/OTUD3","total_profiled":1310},"omim":[{"mim_id":"611758","title":"OTU DOMAIN-CONTAINING PROTEIN 3; OTUD3","url":"https://www.omim.org/entry/611758"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Intermediate filaments","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/OTUD3"},"hgnc":{"alias_symbol":["KIAA0459","DUBA4"],"prev_symbol":[]},"alphafold":{"accession":"Q5T2D3","domains":[{"cath_id":"3.90.70.80","chopping":"17-40_50-202","consensus_level":"high","plddt":90.7057,"start":17,"end":202},{"cath_id":"1.10.8","chopping":"228-276","consensus_level":"high","plddt":81.6437,"start":228,"end":276}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5T2D3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5T2D3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5T2D3-F1-predicted_aligned_error_v6.png","plddt_mean":70.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=OTUD3","jax_strain_url":"https://www.jax.org/strain/search?query=OTUD3"},"sequence":{"accession":"Q5T2D3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5T2D3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5T2D3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5T2D3"}},"corpus_meta":[{"pmid":"26280536","id":"PMC_26280536","title":"Deubiquitylase OTUD3 regulates PTEN stability and suppresses tumorigenesis.","date":"2015","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/26280536","citation_count":165,"is_preprint":false},{"pmid":"31266968","id":"PMC_31266968","title":"The deubiquitylase OTUD3 stabilizes GRP78 and promotes lung tumorigenesis.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31266968","citation_count":110,"is_preprint":false},{"pmid":"32679077","id":"PMC_32679077","title":"Acetylation-Dependent Deubiquitinase OTUD3 Controls MAVS Activation in Innate Antiviral Immunity.","date":"2020","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/32679077","citation_count":84,"is_preprint":false},{"pmid":"34853315","id":"PMC_34853315","title":"Nicotine-mediated OTUD3 downregulation inhibits VEGF-C mRNA decay to promote lymphatic metastasis of human esophageal cancer.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34853315","citation_count":51,"is_preprint":false},{"pmid":"32483383","id":"PMC_32483383","title":"Ubiquitin ligase CHIP regulates OTUD3 stability and suppresses tumour metastasis in lung cancer.","date":"2020","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/32483383","citation_count":50,"is_preprint":false},{"pmid":"35675826","id":"PMC_35675826","title":"Deubiquitinase OTUD3 regulates metabolism homeostasis in response to nutritional stresses.","date":"2022","source":"Cell metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/35675826","citation_count":45,"is_preprint":false},{"pmid":"32571254","id":"PMC_32571254","title":"Tumor suppressor OTUD3 induces growth inhibition and apoptosis by directly deubiquitinating and stabilizing p53 in invasive breast carcinoma cells.","date":"2020","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/32571254","citation_count":37,"is_preprint":false},{"pmid":"35490179","id":"PMC_35490179","title":"Deubiquitylase OTUD3 prevents Parkinson's disease through stabilizing iron regulatory protein 2.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/35490179","citation_count":36,"is_preprint":false},{"pmid":"35675783","id":"PMC_35675783","title":"Opposing effects of deubiquitinase OTUD3 in innate immunity against RNA and DNA viruses.","date":"2022","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/35675783","citation_count":28,"is_preprint":false},{"pmid":"34380780","id":"PMC_34380780","title":"The deubiquitinase OTUD3 stabilizes ACTN4 to drive growth and metastasis of hepatocellular carcinoma.","date":"2021","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/34380780","citation_count":26,"is_preprint":false},{"pmid":"32775453","id":"PMC_32775453","title":"miR-520h Stimulates Drug Resistance to Paclitaxel by Targeting the OTUD3-PTEN Axis in Breast Cancer.","date":"2020","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/32775453","citation_count":26,"is_preprint":false},{"pmid":"37369659","id":"PMC_37369659","title":"Discovery of an OTUD3 inhibitor for the treatment of non-small cell lung cancer.","date":"2023","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/37369659","citation_count":18,"is_preprint":false},{"pmid":"38351178","id":"PMC_38351178","title":"Phosphorylation-dependent deubiquitinase OTUD3 regulates YY1 stability and promotes colorectal cancer progression.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/38351178","citation_count":17,"is_preprint":false},{"pmid":"38996071","id":"PMC_38996071","title":"Deubiquitylase OTUD3 regulates integrated stress response to suppress progression and sorafenib resistance of liver cancer.","date":"2024","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/38996071","citation_count":17,"is_preprint":false},{"pmid":"32395534","id":"PMC_32395534","title":"The expression change of OTUD3-PTEN signaling axis in glioma cells.","date":"2020","source":"Annals of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32395534","citation_count":14,"is_preprint":false},{"pmid":"36966392","id":"PMC_36966392","title":"Proximity labeling reveals OTUD3 as a DNA-binding deubiquitinase of cGAS.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36966392","citation_count":13,"is_preprint":false},{"pmid":"37829187","id":"PMC_37829187","title":"Deubiquitinase OTUD3: a double-edged sword in immunity and disease.","date":"2023","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/37829187","citation_count":12,"is_preprint":false},{"pmid":"38539203","id":"PMC_38539203","title":"Rolapitant treats lung cancer by targeting deubiquitinase OTUD3.","date":"2024","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/38539203","citation_count":12,"is_preprint":false},{"pmid":"37310728","id":"PMC_37310728","title":"Bone Marrow Stromal Cell-Secreted Extracellular Vesicles Containing miR-34c-5p Alleviate Lung Injury and Inflammation in Bronchopulmonary Dysplasia Through Promotion of PTEN Degradation by Targeting OTUD3.","date":"2023","source":"Immunological investigations","url":"https://pubmed.ncbi.nlm.nih.gov/37310728","citation_count":11,"is_preprint":false},{"pmid":"39097608","id":"PMC_39097608","title":"Rupatadine-inhibited OTUD3 promotes DLBCL progression and immune evasion through deubiquitinating MYL12A and PD-L1.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/39097608","citation_count":9,"is_preprint":false},{"pmid":"40716486","id":"PMC_40716486","title":"OTUD3-mediated stabilization of SLC7A11 drives sunitinib resistance by suppressing ferroptosis in clear cell renal cell carcinoma.","date":"2025","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/40716486","citation_count":9,"is_preprint":false},{"pmid":"36173586","id":"PMC_36173586","title":"Silencing of LncRNA SNHG6 protects trophoblast cells through regulating miR-101-3p/OTUD3 axis in unexplained recurrent spontaneous abortion.","date":"2022","source":"Journal of molecular histology","url":"https://pubmed.ncbi.nlm.nih.gov/36173586","citation_count":8,"is_preprint":false},{"pmid":"37107185","id":"PMC_37107185","title":"Deubiquitylase OTUD3 Mediates Endoplasmic Reticulum Stress through Regulating Fortilin Stability to Restrain Dopaminergic Neurons Apoptosis.","date":"2023","source":"Antioxidants (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/37107185","citation_count":7,"is_preprint":false},{"pmid":"40680146","id":"PMC_40680146","title":"OTUD3 prevents ulcerative colitis by inhibiting microbiota-mediated STING activation.","date":"2025","source":"Science immunology","url":"https://pubmed.ncbi.nlm.nih.gov/40680146","citation_count":6,"is_preprint":false},{"pmid":"36503125","id":"PMC_36503125","title":"OTUD3: A Lys6 and Lys63 specific deubiquitinase in early vertebrate development.","date":"2022","source":"Biochimica et biophysica acta. Gene regulatory mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/36503125","citation_count":6,"is_preprint":false},{"pmid":"39415292","id":"PMC_39415292","title":"The deubiquitinase OTUD3 stabilizes IRP2 expression to reduce hippocampal neuron ferroptosis via the p53/PTGS2 pathway to ameliorate cerebral ischemia-reperfusion injury.","date":"2024","source":"European journal of medical research","url":"https://pubmed.ncbi.nlm.nih.gov/39415292","citation_count":6,"is_preprint":false},{"pmid":"38288086","id":"PMC_38288086","title":"OTUD3 suppresses the mTORC1 signaling by deubiquitinating KPTN.","date":"2024","source":"Frontiers in pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/38288086","citation_count":5,"is_preprint":false},{"pmid":"36531510","id":"PMC_36531510","title":"Prevalence and clinical characteristics of T2DM patients with OTUD3 gene rs78466831 SNP at a single academic center in China.","date":"2022","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/36531510","citation_count":5,"is_preprint":false},{"pmid":"40382618","id":"PMC_40382618","title":"OTUD3 inhibits breast cancer cell metastasis by regulating TGF-β pathway through deubiquitinating SMAD7.","date":"2025","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/40382618","citation_count":4,"is_preprint":false},{"pmid":"40462502","id":"PMC_40462502","title":"The deubiquitinase OTUD3 plays a neuroprotective role by reducing ferroptosis induced by cerebral ischaemia reperfusion via stabilizing PLK1 via deubiquitination.","date":"2025","source":"Clinical and translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40462502","citation_count":2,"is_preprint":false},{"pmid":"41155222","id":"PMC_41155222","title":"Roles of Deubiquitinases OTUD3 and OTUD5 in Inflammatory Bowel Diseases.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41155222","citation_count":1,"is_preprint":false},{"pmid":"40181152","id":"PMC_40181152","title":"Phosphorylation enhanced OTUD3 deubiquitination ARID3A promotes the progress of cholangiocarcinoma.","date":"2025","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/40181152","citation_count":1,"is_preprint":false},{"pmid":"40886936","id":"PMC_40886936","title":"Dysregulation of the TNF-α-OTUD3-PPARγ signaling axis exacerbates retinal oxidative stress and inflammation in diabetic retinopathy.","date":"2025","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40886936","citation_count":1,"is_preprint":false},{"pmid":"39788523","id":"PMC_39788523","title":"Research progress in deubiquitinase OTUD3.","date":"2024","source":"Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39788523","citation_count":0,"is_preprint":false},{"pmid":"41437362","id":"PMC_41437362","title":"The dual role of OTUD3 in cancer: mechanisms and therapeutic implications.","date":"2025","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/41437362","citation_count":0,"is_preprint":false},{"pmid":"41067575","id":"PMC_41067575","title":"Pathogenic OTUD3 Mutations Predispose to Ulcerative Colitis Due to Barrier Dysfunction.","date":"2025","source":"Cellular and molecular gastroenterology and hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/41067575","citation_count":0,"is_preprint":false},{"pmid":"41146402","id":"PMC_41146402","title":"A Variant of OTUD3 in Early-Onset Parkinsonism.","date":"2025","source":"Neuropathology and applied neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/41146402","citation_count":0,"is_preprint":false},{"pmid":"41484895","id":"PMC_41484895","title":"BHLHE22, targeted by deubiquitinating enzyme OTUD3, exerts an antitumor role in triple-negative breast cancer progression via transcriptionally inhibiting CDT1.","date":"2026","source":"Breast cancer research : BCR","url":"https://pubmed.ncbi.nlm.nih.gov/41484895","citation_count":0,"is_preprint":false},{"pmid":"41999888","id":"PMC_41999888","title":"The E3 ligase β-TRCP1 earmarks OTUD3 for destruction to fine-tune cGAS activation.","date":"2026","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41999888","citation_count":0,"is_preprint":false},{"pmid":"41640247","id":"PMC_41640247","title":"Targeted Mitochondrial ECSIT Overexpression Attenuates MASH by Increasing OTUD3 Expression.","date":"2026","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/41640247","citation_count":0,"is_preprint":false},{"pmid":"41763483","id":"PMC_41763483","title":"OTUD3-mediated deubiquitination licenses TEX264 to orchestrate ER-phagy for KDM5B degradation in teniposide lung cancer therapy.","date":"2026","source":"European journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41763483","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":22724,"output_tokens":6842,"usd":0.085401,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":15893,"output_tokens":4395,"usd":0.09467,"stage2_stop_reason":"end_turn"},"total_usd":0.180071,"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\": 2015,\n      \"finding\": \"OTUD3 directly interacts with PTEN, de-polyubiquitylates it, and stabilizes PTEN protein levels. Depletion of OTUD3 leads to activation of Akt signaling and promotes cellular transformation. Loss-of-function OTUD3 mutations found in human cancers either abolish catalytic activity or attenuate interaction with PTEN.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, OTUD3 transgenic mice, loss-of-function mutant analysis, in vitro deubiquitylation assay\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (Co-IP, in vitro DUB assay, transgenic mouse model, catalytic mutants) in a single rigorous study\",\n      \"pmids\": [\"26280536\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"OTUD3 interacts with, deubiquitylates, and stabilizes GRP78 (glucose-regulated protein 78 kDa) in lung cancer cells, promoting lung tumorigenesis. In vivo deletion of OTUD3 slows KrasG12D-driven lung adenocarcinoma progression.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, OTUD3 knockout mice with KrasG12D lung cancer model, knockdown/rescue experiments\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — reciprocal Co-IP, ubiquitination assay, and in vivo mouse genetic model with defined phenotypic readout\",\n      \"pmids\": [\"31266968\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"OTUD3 directly hydrolyzes K63-linked polyubiquitination of MAVS to suppress innate antiviral immune signaling. The catalytic activity of OTUD3 is regulated by acetylation of Lys129; SIRT1 removes this acetylation upon virus infection, inactivating OTUD3 and permitting antiviral immunity.\",\n      \"method\": \"In vitro deubiquitylation assay, acetylation site mutagenesis (K129 mutants), OTUD3-deficient mice, SIRT1 knockdown/overexpression, viral infection models\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro DUB assay with linkage specificity, acetylation site mutagenesis, and in vivo mouse knockout model with orthogonal methods\",\n      \"pmids\": [\"32679077\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"OTUD3 directly interacts with p53, deubiquitylates it, and protects p53 from MDM2-mediated ubiquitination and degradation. The catalytically inactive OTUD3 mutant fails to stabilize p53. The interaction occurs through the amino-terminal OTU region of OTUD3.\",\n      \"method\": \"Co-immunoprecipitation, GST pulldown, ubiquitination assay, half-life analysis, catalytic mutant (inactive mutant), proliferation and apoptosis assays\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and GST pulldown plus ubiquitination assay in single lab, multiple orthogonal methods\",\n      \"pmids\": [\"32571254\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CHIP (carboxyl terminus of Hsc70-interacting protein) is an E3 ubiquitin ligase for OTUD3; CHIP interacts with OTUD3, polyubiquitylates it, and promotes OTUD3 proteasomal degradation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, CHIP knockdown/overexpression, CHIP catalytic mutant analysis\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and ubiquitination assay in single lab with multiple methods\",\n      \"pmids\": [\"32483383\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"OTUD3 directly interacts with ZFP36 and stabilizes it by inhibiting FBXW7-mediated K48-linked polyubiquitination. ZFP36 in turn binds VEGF-C 3'-UTR and recruits RNA degrading complex to promote VEGF-C mRNA decay.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, RNA decay assay, ZFP36 rescue experiments, esophageal cancer cell and in vivo models\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, and functional mRNA decay readout in single lab\",\n      \"pmids\": [\"34853315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"OTUD3 directly binds ACTN4 (alpha-actinin 4) and deubiquitinates it to stabilize ACTN4 protein, driving hepatocellular carcinoma growth and metastasis.\",\n      \"method\": \"Mass spectrometry identification, Co-immunoprecipitation, ubiquitination assay, gain- and loss-of-function assays, xenograft mouse model\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS identification plus Co-IP and ubiquitination assay, single lab\",\n      \"pmids\": [\"34380780\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUD3 functions as a deubiquitylase for IRP2 (iron regulatory protein 2), interacting with IRP2 in the cytoplasm, removing polyubiquitin to stabilize IRP2 in an iron-independent manner. OTUD3 knockout mice display nigral iron accumulation, motor deficits, and nigrostriatal dopaminergic neurodegeneration resembling Parkinson's disease pathology.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, OTUD3 knockout mouse model, neurochemical and behavioral analyses\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — Co-IP, ubiquitination assay, and in vivo knockout mouse model with defined neurodegeneration phenotype\",\n      \"pmids\": [\"35490179\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUD3 binds to RIG-I and MDA5, removing K63-linked ubiquitination to reduce their binding to viral RNA and the adaptor MAVS, suppressing RNA virus-triggered innate immunity. Simultaneously, OTUD3 associates with cGAS and removes K48-linked ubiquitination at Lys279, stabilizing cGAS and enhancing its DNA-binding ability, thus promoting DNA virus-triggered innate immunity.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with linkage-specific analysis, Otud3-deficient mice and zebrafish, viral infection models (RNA and DNA viruses)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple substrates identified with linkage-specific DUB activity, validated in both mouse and zebrafish in vivo models\",\n      \"pmids\": [\"35675783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUD3 cleaves preferentially K6- and K63-linked polyubiquitin chains (not primarily degradative linkages). In cells, OTUD3 is present in the cytoplasm where it can bind to microtubules. In Xenopus embryos, Otud3 deficiency impairs cranial neural crest-derived structures and causes movement defects.\",\n      \"method\": \"In vitro deubiquitylation assay with linkage-specific ubiquitin chains, cellular fractionation/immunofluorescence for microtubule co-localization, Xenopus morpholino knockdown\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro DUB assay with linkage specificity and in vivo Xenopus model, single lab\",\n      \"pmids\": [\"36503125\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"OTUD3 is regulated by glucose and fatty acid signals through CBP-dependent acetylation, which promotes OTUD3 nuclear translocation. In the nucleus, OTUD3 stabilizes PPARδ by deubiquitination, regulating genes involved in glucose and lipid metabolism and oxidative phosphorylation. A c.863G>A OTUD3 mutation reduces protein stability and catalytic activity and is found in a family with early-onset diabetes.\",\n      \"method\": \"Otud3-/- mouse model with high-fat diet, acetylation mutant analysis, nuclear fractionation/immunofluorescence, ubiquitination assay for PPARδ, PPARδ agonist rescue experiment\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vivo knockout mouse model, acetylation site mutagenesis, nuclear translocation assay, and substrate ubiquitination assay with pharmacological rescue\",\n      \"pmids\": [\"35675826\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"OTUD3 is recruited to cytosolic cGAS-DNA complexes through its ability to directly bind DNA. In addition to stabilizing cGAS (removing ubiquitin to prevent degradation), OTUD3 enhances cGAS enzymatic activity, thereby promoting anti-DNA virus immune response.\",\n      \"method\": \"Proximity labeling (TurboID) of cGAS to identify interactors, Co-immunoprecipitation, in vitro DNA-binding assay, cGAS enzymatic activity assay, viral infection assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proximity labeling plus Co-IP and enzymatic activity assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"36966392\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"OTUD3 regulates the ubiquitination level of Fortilin through its OTU domain, stabilizing Fortilin, which in turn maintains Fortilin-IRE1α interaction. OTUD3 knockdown reduces Fortilin-IRE1α interaction, enhancing IRE1α activity and promoting ER stress-induced apoptosis of dopaminergic neurons.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, OTUD3 knockout mouse histology, IRE1α inhibitor rescue (STF-083010), ER stress marker analysis (PDI, XBP1s)\",\n      \"journal\": \"Antioxidants (Basel, Switzerland)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ubiquitination assay with pharmacological rescue in single lab\",\n      \"pmids\": [\"37107185\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"OTUD3 is a deubiquitylase of eIF2α (eukaryotic initiation factor 2α), removing K27-linked polyubiquitylation from eIF2α. This decreases interactions between eIF2α and the kinase EIF2AK3 (PERK), thereby antagonizing the integrated stress response (ISR) and suppressing liver cancer progression.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with K27-linkage specificity, OTUD3 deficient mice with N-nitrosodiethylamine-induced HCC, ISRIB pharmacological rescue\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — linkage-specific ubiquitination assay, in vivo knockout mouse model of HCC, and pharmacological rescue with multiple orthogonal methods\",\n      \"pmids\": [\"38996071\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PLK1 mediates phosphorylation of OTUD3 at Ser326, which enhances OTUD3 binding to and deubiquitination of YY1 transcription factor, stabilizing YY1 and promoting colorectal cancer progression.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, PLK1 kinase assay, phospho-site mutant analysis (S326), colorectal cancer cell proliferation assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, and phosphorylation site mutagenesis in single lab\",\n      \"pmids\": [\"38351178\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"OTUD3 deubiquitinates SLC7A11, protecting it from proteasomal degradation, thereby promoting cystine transport, reducing intracellular ROS levels, and suppressing ferroptosis to drive sunitinib resistance in clear cell renal cell carcinoma.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, ferroptosis assay (ROS levels), sunitinib resistance cell models and in vivo xenograft\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ubiquitination assay with functional ferroptosis readout, single lab\",\n      \"pmids\": [\"40716486\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"OTUD3 deubiquitinates and stabilizes KPTN (kaptin), acting through its OTU domain. Ubiquitination of KPTN primarily occurs at lysine 49 and is a non-degradative functional modification. OTUD3 promotes GATOR1 lysosomal localization via KPTN, thereby suppressing mTORC1 signaling activation independent of PTEN.\",\n      \"method\": \"In vivo ubiquitination assay, Co-immunoprecipitation, CRISPR/Cas9 OTUD3 knockout, immunofluorescence for GATOR1 localization, NMR, mTORC1 signaling readout (S6K phosphorylation)\",\n      \"journal\": \"Frontiers in pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo ubiquitination assay, CRISPR knockout, and localization imaging in single lab\",\n      \"pmids\": [\"38288086\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"OTUD3 deubiquitinates PLK1 via K48-linked ubiquitin chains, stabilizing PLK1 protein. Stabilized PLK1 activates the PI3K/AKT signaling pathway, reducing ferroptosis after cerebral ischemia-reperfusion injury. OTUD3 binds the amino acid sequence 35-305 of PLK1.\",\n      \"method\": \"Co-immunoprecipitation-mass spectrometry, ubiquitination assay (K48-linkage specific), OTUD3 overexpression/knockdown in OGD/R neuron model, PLK1 inhibitor rescue, in vivo cerebral I/R mouse model\",\n      \"journal\": \"Clinical and translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP-MS and ubiquitination assay with functional pathway readout, single lab\",\n      \"pmids\": [\"40462502\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUD3 deubiquitinates STING in intestinal fibroblasts to suppress pathological STING activation triggered by microbial cyclic GMP-AMP (cGAMP). Mice harboring a UC-risk missense variant in Otud3 show pathological features of ulcerative colitis after fecal microbiota transplantation from UC patients.\",\n      \"method\": \"OTUD3 knockout and missense variant knock-in mice, fecal microbiota transplantation, ubiquitination assay for STING, intestinal fibroblast functional assays\",\n      \"journal\": \"Science immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vivo mouse genetic models (KO and knock-in variant), ubiquitination assay, and functional microbiota transplant challenge\",\n      \"pmids\": [\"40680146\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"GSK3β phosphorylates OTUD3 at Ser9, which enhances OTUD3 affinity for ARID3A and further stabilizes ARID3A by removing ubiquitin chains at K240 and K329 of ARID3A, promoting cholangiocarcinoma progression.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, site-specific mutagenesis (K240/K329 of ARID3A, Ser9 of OTUD3), in vivo and in vitro CCA proliferation/metastasis assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay with site mutagenesis, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"40181152\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The E3 ubiquitin ligase β-TRCP1 targets OTUD3 for ubiquitination and proteasomal degradation through RSK3-mediated phosphorylation of a conserved 'ESG' degron motif in OTUD3. Cytosolic DNA challenge inactivates the β-TRCP1/RSK3 pathway (via mTORC2 signaling, independently of canonical Ras/MEK/ERK and DNA damage kinases), resulting in OTUD3 stabilization and enhanced cGAS activation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, phospho-degron mutagenesis (ESG motif), RSK3 kinase assay, mTORC2 inhibitor experiments, viral/DNA challenge cell assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, mutagenesis of phospho-degron, and kinase/pathway inhibitor dissection in single lab\",\n      \"pmids\": [\"41999888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUD3 deubiquitinates and stabilizes SMAD7, thereby inhibiting TGF-β signaling, suppressing EMT, and reducing breast cancer cell invasion. Catalytically inactive OTUD3 (C76 site mutant) fails to regulate BHLHE22 and SMAD7 protein stability.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, catalytic mutant (C76), luciferase reporter assay for TGF-β pathway, transwell invasion assay, 3D matrigel culture\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, and catalytic site mutagenesis with functional invasion readout, single lab\",\n      \"pmids\": [\"40382618\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUD3 deubiquitinates MYL12A and PD-L1 to enhance cell survival and immune evasion (CD8+ T cell exhaustion) in DLBCL. The OTUD3 inhibitor Rupatadine competitively binds OTUD3 and diminishes deubiquitination of both MYL12A and PD-L1.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, competitive binding assay for Rupatadine-OTUD3, CD8+ T cell co-culture exhaustion assay\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ubiquitination assay with functional immune cell readout, single lab\",\n      \"pmids\": [\"39097608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"OTUD3 deubiquitinates and stabilizes PPARγ in retinal pigment epithelium cells, protecting against oxidative stress and inflammation in diabetic retinopathy.\",\n      \"method\": \"OTUD3 knockdown/knockout mouse model, ubiquitination assay for PPARγ, PPARγ agonist rescue, ROS/apoptosis assays in RPE cell lines\",\n      \"journal\": \"Life sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, PPARγ as substrate supported by knockdown and agonist rescue but limited direct ubiquitination mechanistic detail in abstract\",\n      \"pmids\": [\"40886936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"OTUD3 deubiquitinates and stabilizes BHLHE22 transcription factor in triple-negative breast cancer, suppressing tumor progression. The catalytic C76 mutant of OTUD3 fails to stabilize BHLHE22. BHLHE22 mediates the antitumor effect of OTUD3 by transcriptionally inhibiting CDT1.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, catalytic site mutant (C76), dual luciferase reporter assay for CDT1 transcription, mRNA-seq, in vivo xenograft\",\n      \"journal\": \"Breast cancer research : BCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ubiquitination assay with catalytic mutant and transcriptional readout, single lab\",\n      \"pmids\": [\"41484895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Mitochondrial ECSIT promotes the localization of OTUD3 to mitochondria, where OTUD3 deubiquitinates SIRT3 to stabilize it, thereby inhibiting mtDNA oxidation and alleviating MASH-associated metabolic disorders.\",\n      \"method\": \"ECSIT mitochondria-targeted transgenic mice, OTUD3 mitochondrial fractionation/immunofluorescence, ubiquitination assay for SIRT3, HFHC and MCD diet MASH models\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo transgenic mouse model with fractionation and ubiquitination assay, single lab\",\n      \"pmids\": [\"41640247\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"OTUD3 deubiquitinates and stabilizes TEX264, a receptor for ER-phagy. Stabilized TEX264 enables ER-phagy-mediated degradation of KDM5B in lung cancer cells treated with teniposide. OTUD3 silencing dampens teniposide-driven ER-phagy and KDM5B inhibition.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, OTUD3 knockdown, ER-phagy flux assay, lung cancer organoid and xenograft models\",\n      \"journal\": \"European journal of pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, and functional ER-phagy readout in single lab\",\n      \"pmids\": [\"41763483\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"OTUD3 is a cytoplasmic OTU-family deubiquitinase with a strong preference for K6, K27, K48, and K63-linked polyubiquitin chains that stabilizes a wide array of substrates (PTEN, GRP78, IRP2, p53, MAVS, cGAS, eIF2α, ACTN4, ZFP36, SMAD7, YY1, KPTN, PPARδ, SLC7A11, PLK1, TEX264, SIRT3, and others) by removing polyubiquitin to prevent proteasomal degradation; its catalytic activity is tightly regulated by reversible acetylation at Lys129 (controlled by CBP and SIRT1) and by phosphorylation-dependent degron recognition (RSK3/β-TRCP1 axis and PLK1/GSK3β-mediated priming), placing OTUD3 as a context-dependent hub that can suppress or promote tumorigenesis depending on which substrate dominates in a given tissue, and that controls innate antiviral/DNA-sensing immunity, iron homeostasis, integrated stress response, and metabolic regulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"OTUD3 is an OTU-family deubiquitinase that removes polyubiquitin from a broad set of substrates to control their stability and activity, positioning it as a context-dependent regulator of tumorigenesis, innate immunity, and metabolism [#0, #2, #10]. It hydrolyzes specific ubiquitin linkages\\u2014preferentially K6- and K63-linked chains in vitro\\u2014and resides largely in the cytoplasm, where it can associate with microtubules [#9]. Its substrate scope spans tumor-suppressive targets such as PTEN, whose stabilization restrains Akt signaling and transformation [#0], p53, which it protects from MDM2-mediated degradation [#3], and SMAD7 [#21], as well as pro-tumorigenic targets including GRP78 in lung cancer [#1] and ACTN4 in hepatocellular carcinoma [#6], explaining its dual roles across tissues. In innate immunity OTUD3 acts bidirectionally: it strips K63-linked ubiquitin from MAVS, RIG-I, and MDA5 to dampen RNA-virus signaling [#2, #8], while binding DNA and cGAS to remove K48-linked ubiquitin and enhance cGAS enzymatic activity, thereby promoting DNA-sensing immunity [#8, #11], and it restrains pathological STING activation in intestinal fibroblasts [#18]. OTUD3 also stabilizes IRP2 to govern iron homeostasis, with its loss producing nigral iron accumulation and dopaminergic neurodegeneration [#7], and antagonizes the integrated stress response by deubiquitinating eIF2\\u03b1 [#13]. Its activity is tightly regulated by post-translational control: reversible Lys129 acetylation governs catalytic activity and CBP-driven nuclear translocation toward metabolic substrates such as PPAR\\u03b4 [#2, #10], CHIP and the RSK3/\\u03b2-TRCP1 axis target it for degradation [#4, #20], and PLK1- and GSK3\\u03b2-mediated phosphorylation redirect its substrate engagement [#14, #19]. An OTUD3 missense variant linked to early-onset diabetes reduces protein stability and catalytic activity [#10], and a UC-risk variant predisposes mice to ulcerative colitis-like pathology [#18].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Established OTUD3 as a functional deubiquitinase with a defined substrate by showing it directly stabilizes PTEN to restrain Akt-driven transformation, framing OTUD3 as a tumor suppressor.\",\n      \"evidence\": \"Co-IP, in vitro DUB assay, transgenic mice, and cancer-associated loss-of-function mutants\",\n      \"pmids\": [\"26280536\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Linkage specificity on PTEN not defined\", \"Whether PTEN is the dominant substrate in all tissues unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed that OTUD3 can also be pro-tumorigenic by stabilizing GRP78, showing its role is substrate- and tissue-context dependent rather than uniformly tumor-suppressive.\",\n      \"evidence\": \"Reciprocal Co-IP, ubiquitination assay, and OTUD3 knockout in a KrasG12D lung adenocarcinoma mouse model\",\n      \"pmids\": [\"31266968\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism reconciling opposing PTEN vs GRP78 roles not addressed\", \"Ubiquitin linkage on GRP78 not specified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified acetylation at Lys129 as a switch controlling OTUD3 catalytic activity and connected OTUD3 to innate antiviral signaling via K63-linked deubiquitination of MAVS.\",\n      \"evidence\": \"In vitro DUB assay, K129 acetylation mutants, SIRT1 manipulation, and OTUD3-deficient mice with viral infection\",\n      \"pmids\": [\"32679077\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How acetylation alters catalytic geometry not structurally defined\", \"CBP as the writer not established in this study\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended the tumor-suppressor model by showing OTUD3 stabilizes p53 against MDM2, and identified CHIP as an E3 ligase that degrades OTUD3, defining its turnover control.\",\n      \"evidence\": \"Co-IP, GST pulldown, ubiquitination and half-life assays (p53); reciprocal Co-IP and ubiquitination with CHIP mutants\",\n      \"pmids\": [\"32571254\", \"32483383\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab findings without in vivo confirmation\", \"Linkage type of CHIP-mediated chains not specified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined OTUD3's intrinsic linkage preference (K6/K63), cytoplasmic/microtubule localization, and roles in iron homeostasis and DNA/RNA virus sensing, establishing the bidirectional immune function and a neurodegeneration phenotype.\",\n      \"evidence\": \"Linkage-specific in vitro DUB assays, fractionation/IF, IRP2 and RIG-I/MDA5/cGAS ubiquitination assays, OTUD3 knockout mice and zebrafish, Xenopus knockdown\",\n      \"pmids\": [\"35490179\", \"35675783\", \"36503125\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How a single DUB selects opposing immune substrates (RIG-I vs cGAS) mechanistically unclear\", \"Microtubule binding functional consequence undefined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed acetylation directs OTUD3 to the nucleus to stabilize PPAR\\u03b4 for metabolic gene control, and linked an OTUD3 mutation to early-onset diabetes, broadening OTUD3 beyond cytoplasmic functions.\",\n      \"evidence\": \"Otud3-/- mice on high-fat diet, acetylation mutants, nuclear fractionation/IF, PPAR\\u03b4 ubiquitination assay with agonist rescue, human family mutation\",\n      \"pmids\": [\"35675826\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Acetyltransferase/deacetylase pairing for nuclear translocation incomplete\", \"Causality of the c.863G>A variant at population scale not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mechanistically deepened the cGAS axis by demonstrating OTUD3 directly binds DNA to be recruited to cGAS-DNA complexes and enhances cGAS enzymatic activity beyond mere stabilization.\",\n      \"evidence\": \"TurboID proximity labeling, Co-IP, in vitro DNA-binding and cGAS activity assays, viral infection\",\n      \"pmids\": [\"36966392\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of DNA binding not resolved\", \"Single-lab enzymatic enhancement awaits independent confirmation\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Diversified substrate repertoire and regulatory inputs: OTUD3 antagonizes the integrated stress response via K27-linked deubiquitination of eIF2\\u03b1, and phosphorylation by PLK1 (Ser326) and stabilization of PLK1, KPTN, and SLC7A11 connect OTUD3 to mTORC1, ferroptosis, and cell-cycle control.\",\n      \"evidence\": \"Linkage-specific ubiquitination assays, knockout HCC mice with ISRIB rescue, kinase assays, phospho-site mutants, and functional ferroptosis/mTORC1 readouts\",\n      \"pmids\": [\"38996071\", \"38351178\", \"38288086\", \"40716486\", \"40462502\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Many substrate relationships rest on single-lab data\", \"How phosphorylation reshapes substrate selection not generalized\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Mapped degron-based turnover (RSK3/\\u03b2-TRCP1 via an ESG motif), GSK3\\u03b2 priming for ARID3A engagement, and expanded immune/metabolic/cancer substrates (STING, SMAD7, PPAR\\u03b3, MYL12A/PD-L1), reinforcing OTUD3 as a heavily PTM-gated hub with therapeutic targetability.\",\n      \"evidence\": \"Phospho-degron mutagenesis with mTORC2 inhibitors, site-specific ubiquitination assays, knock-in UC-variant mice with fecal transplant, catalytic-mutant invasion assays, and Rupatadine competitive-binding/T-cell exhaustion assays\",\n      \"pmids\": [\"40680146\", \"40181152\", \"40382618\", \"39097608\", \"41999888\", \"40886936\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Disease-variant causality (UC) established only in mouse models\", \"PPAR\\u03b3 substrate relationship is low-confidence with limited direct ubiquitination detail\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Localized OTUD3 to additional compartments and pathways: ECSIT-dependent mitochondrial recruitment to stabilize SIRT3, and stabilization of BHLHE22 and the ER-phagy receptor TEX264, linking OTUD3 to mitochondrial protection, ER-phagy, and tumor suppression.\",\n      \"evidence\": \"Mitochondria-targeted transgenic mice with fractionation and SIRT3 ubiquitination assay; Co-IP, catalytic mutants, transcriptional and ER-phagy flux readouts in cancer models\",\n      \"pmids\": [\"41640247\", \"41484895\", \"41763483\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mitochondrial vs nuclear vs cytoplasmic targeting determinants not unified\", \"Single-lab substrate claims lacking cross-validation\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How OTUD3 selects among its many substrates and opposing roles in a given tissue\\u2014and whether a unifying structural or regulatory logic governs its linkage specificity and subcellular partitioning\\u2014remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model integrating PTM-driven substrate switching\", \"No systematic comparison of which substrate dominates per tissue\", \"Therapeutic window of OTUD3 inhibition across opposing functions undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3, 7, 8, 13]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 2, 9, 13]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [7, 9, 11]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [25]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [2, 8, 11, 18, 22]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 1, 6, 7, 13]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [7, 10, 25]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 2, 13]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PTEN\", \"GRP78\", \"MAVS\", \"cGAS\", \"IRP2\", \"p53\", \"CHIP\", \"PPARD\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}