{"gene":"USP45","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2014,"finding":"USP45 associates with ERCC1 (a subunit of the XPF-ERCC1 DNA repair endonuclease) via a short acidic motif outside the USP45 catalytic domain, and directly deubiquitylates ERCC1 in vitro. USP45 knockout cells show markedly elevated ubiquitylated ERCC1 and are hypersensitive to UV irradiation and DNA interstrand cross-links, similar to ERCC1-deficient cells. ERCC1 translocation to DNA damage-induced subnuclear foci is impaired in USP45 knockout cells. USP45 itself localizes to sites of DNA damage in a manner dependent on its deubiquitylase activity but independent of ERCC1-XPF binding.","method":"In vitro deubiquitylation assay, Co-IP, mutant analysis (catalytic-dead and ERCC1-binding-deficient USP45), knockout cell lines, UV/ICL sensitivity assays, immunofluorescence of subnuclear foci","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro deubiquitylation assay with mutagenesis, reciprocal binding studies, KO cells with multiple orthogonal phenotypic readouts in a single rigorous study","pmids":["25538220"],"is_preprint":false},{"year":2018,"finding":"USP45 forms a complex with Spindly (identified by mass spectrometry), and this interaction depends on the catalytic activity of USP45. USP45 preferentially cleaves K48-linked ubiquitin chains and potentially K6-linked chains. Spindly is mono-ubiquitylated, and this modification is specifically removed by catalytically active but not catalytic-inactive USP45. Loss of USP45 impairs cell migration, similar to loss of Spindly.","method":"Mass spectrometry-based interactome, Co-IP, in vitro deubiquitylation assay with catalytic-dead mutant, cell migration assay (knockdown)","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — MS identification plus Co-IP and in vitro activity assay, single lab, multiple orthogonal methods","pmids":["30258100"],"is_preprint":false},{"year":2016,"finding":"Morpholino-mediated knockdown of usp45 in zebrafish causes abnormal retinal development with defective formation of retinal structures, establishing a functional role for USP45 in vertebrate retina differentiation.","method":"Morpholino knockdown in zebrafish embryos, phenotypic analysis of retinal morphology","journal":"Methods in molecular biology (Clifton, N.J.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — zebrafish KD with defined cellular phenotype; single lab, single model organism","pmids":["27613029"],"is_preprint":false},{"year":2018,"finding":"Biallelic loss-of-function mutations in USP45 cause Leber congenital amaurosis. USP45 protein is enriched in the inner segments of photoreceptors (human and zebrafish retina). usp45 morpholino knockdown in zebrafish causes abnormal retinal development rescued by wild-type usp45 mRNA. Targeted knockout of Usp45 in mice produces abnormal electroretinography responses consistent with LCA.","method":"Whole-exome sequencing, immunohistochemistry for localization, zebrafish morpholino knockdown with mRNA rescue, mouse knockout with ERG functional readout","journal":"Journal of medical genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal models (zebrafish KD with rescue, mouse KO with functional ERG), localization by IHC, replication of retinal phenotype across two species","pmids":["30573563"],"is_preprint":false},{"year":2023,"finding":"USP45 directly binds MYC and deubiquitinates/stabilizes it, preventing its proteasomal degradation. USP45 overexpression upregulates MYC and enhances cancer cell stemness and drug resistance. The natural small molecule α-mangostin specifically binds and inhibits USP45, suppressing USP45-induced stemness and drug resistance in vitro and in a cervical cancer xenograft model.","method":"Co-IP/GST pulldown, in vitro deubiquitination assay, USP45 overexpression/shRNA knockdown, MYC shRNA epistasis, xenograft mouse model, binding assay with α-mangostin","journal":"Cancers","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct binding and in vitro deubiquitination assay reported, epistasis with MYC shRNA, single lab","pmids":["36765885"],"is_preprint":false},{"year":2023,"finding":"MYH10 combines with MYH9 to recruit USP45, which then deubiquitinates Snail, preventing its degradation and promoting EMT, tumorigenesis, and cisplatin resistance in serous ovarian cancer. Interaction was established by Co-IP and GST pulldown.","method":"Co-IP, GST pulldown, confocal co-localization, knockdown of MYH10 in vitro and in vivo, MYH10/MYH9/Snail epistasis","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP and GST pulldown for interaction, single lab, in vivo xenograft confirmation of phenotype","pmids":["36929633"],"is_preprint":false},{"year":2025,"finding":"USP45 interacts with and deubiquitinates Coronin 1B (Coro1B), stabilizing Coro1B protein levels. Loss of USP45 or Coro1B promotes formation of F-actin patches and translocation of V-ATPase to lysosomes in an N-WASP-dependent manner, leading to increased lysosomal acidification, enhanced lysosomal function, and autophagy activation. This pathway was demonstrated in both Drosophila and mammalian cells.","method":"Co-IP, in vitro deubiquitination assay, USP45/Coro1B KO/KD, F-actin imaging, V-ATPase localization assay, lysosomal acidification assay, autophagy flux assay in Drosophila and mammalian cells","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — Co-IP plus in vitro deubiquitination, genetic epistasis (N-WASP dependence), multiple orthogonal readouts, replicated across two model systems","pmids":["40067150"],"is_preprint":false},{"year":2025,"finding":"USP45 directly interacts with and deubiquitinates both RTCB and DDX1, removing polyubiquitin chains and stabilizing these proteins. USP45-mediated DDX1 deubiquitination requires RTCB (asymmetric regulatory hierarchy), whereas RTCB deubiquitination is DDX1-independent. This USP45-RTCB-DDX1 axis promotes cell proliferation and chemoresistance in cellular and murine models.","method":"Co-IP, co-localization, in vitro deubiquitination assay, epistasis using RTCB/DDX1 knockdown, xenograft mouse model","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct in vitro deubiquitination and Co-IP reported, asymmetric epistasis established, single lab","pmids":["41468936"],"is_preprint":false},{"year":2025,"finding":"USP45's catalytic domain directly binds the N-terminus of MRGPRF and stabilizes MRGPRF, specifically by removing K63-linked ubiquitination from MRGPRF in melanoma cells. USP45 overexpression inhibits melanoma cell malignancy via MRGPRF, and MRGPRF depletion mitigates USP45's anti-melanoma effects; MRGPRF overexpression rescues the enhanced malignancy caused by USP45 deficiency.","method":"Screening of 40 USPs, Co-IP, in vitro deubiquitination assay (K63-chain specificity), domain mapping, epistasis via MRGPRF KD/OE, xenograft mouse model","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — in vitro deubiquitination with chain-type specificity, genetic epistasis, single lab","pmids":["40788071"],"is_preprint":false},{"year":2026,"finding":"USP45 specifically deubiquitinates HIV-1 Tat at lysine 19, targeting both K48-linked and K63-linked ubiquitin chains. USP45 overexpression suppresses Tat-dependent HIV-1 transcriptional activation and viral particle production, while USP45 knockdown enhances both. USP45 primarily inhibits the initial stages of viral transcription in latently infected cells. USP45 expression is induced by interferons, identifying it as an interferon-stimulated gene.","method":"NanoBRET-based DUB screening, Co-IP, in vitro deubiquitination assay with site-specific mapping (K19), USP45 overexpression/knockdown, HIV-1 transcription assay, digital PCR in latently infected cells, interferon stimulation","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — site-specific deubiquitination mapping and functional transcription assay, multiple orthogonal methods, single lab","pmids":["41668887"],"is_preprint":false}],"current_model":"USP45 is a catalytically active deubiquitylase (DUB) that stabilizes multiple substrates—including ERCC1, Spindly, MYC, Snail, Coronin 1B, MRGPRF, RTCB, DDX1, and HIV-1 Tat—by removing ubiquitin chains (with preferences for K48, K63, or K6 linkages depending on substrate), thereby regulating DNA damage repair (via XPF-ERCC1 recruitment to damage foci), autophagy and lysosomal function (via Coronin 1B/actin/V-ATPase axis), cell migration (via Spindly), retinal photoreceptor maintenance, and oncogenic pathways including EMT (Snail), stemness (MYC), and anti-melanoma signaling (MRGPRF)."},"narrative":{"mechanistic_narrative":"USP45 is a catalytically active deubiquitylase that controls the stability and localization of diverse substrates by removing ubiquitin chains, with linkage preferences (K48, K63, K6) that vary by target [PMID:25538220, PMID:30258100, PMID:40788071]. In genome maintenance, USP45 associates with ERCC1 through an acidic motif outside its catalytic domain and directly deubiquitylates ERCC1; loss of USP45 elevates ubiquitylated ERCC1, impairs ERCC1 recruitment to DNA damage foci, and sensitizes cells to UV and interstrand cross-links, while USP45 itself localizes to damage sites in an activity-dependent manner [PMID:25538220]. Biallelic loss-of-function mutations in USP45 cause Leber congenital amaurosis, consistent with its enrichment in photoreceptor inner segments and the retinal phenotypes produced by zebrafish knockdown (rescued by wild-type mRNA) and mouse knockout [PMID:30573563]. Beyond these roles, USP45 acts broadly as a substrate-stabilizing DUB: it deubiquitylates Coronin 1B to restrain F-actin/V-ATPase-driven lysosomal acidification and autophagy [PMID:40067150], stabilizes Spindly to support cell migration [PMID:30258100], and stabilizes oncogenic and signaling substrates including MYC, Snail, the RTCB-DDX1 axis, and MRGPRF, and removes ubiquitin from HIV-1 Tat as an interferon-stimulated gene [PMID:36765885, PMID:36929633, PMID:41468936, PMID:40788071, PMID:41668887].","teleology":[{"year":2014,"claim":"Established USP45 as a bona fide deubiquitylase with a defined substrate (ERCC1) and a concrete role in nucleotide excision/cross-link repair, answering whether USP45 has enzymatic function and a biological context.","evidence":"In vitro deubiquitylation, Co-IP, catalytic-dead and binding-deficient mutants, knockout cells with UV/ICL sensitivity and foci imaging","pmids":["25538220"],"confidence":"High","gaps":["Linkage specificity of ERCC1 chains not defined","Mechanism of USP45 recruitment to damage sites independent of ERCC1-XPF unresolved"]},{"year":2016,"claim":"Provided the first in vivo developmental role for USP45, showing it is required for vertebrate retinal differentiation.","evidence":"Morpholino knockdown in zebrafish with retinal morphology analysis","pmids":["27613029"],"confidence":"Medium","gaps":["No molecular substrate linked to the retinal phenotype","Morpholino specificity not controlled by rescue in this report"]},{"year":2018,"claim":"Connected USP45 to cytoskeletal/migration biology by identifying Spindly as a catalytic-activity-dependent substrate and defining linkage preference (K48, possibly K6).","evidence":"Mass spectrometry interactome, Co-IP, in vitro deubiquitylation with catalytic-dead mutant, migration assay on knockdown","pmids":["30258100"],"confidence":"Medium","gaps":["Functional consequence of Spindly mono-ubiquitin removal on its known roles not mapped","Single-lab finding"]},{"year":2018,"claim":"Established USP45 as a human disease gene, demonstrating that biallelic loss-of-function causes Leber congenital amaurosis with cross-species replication.","evidence":"Whole-exome sequencing, IHC localization, zebrafish knockdown with mRNA rescue, mouse knockout with ERG","pmids":["30573563"],"confidence":"High","gaps":["Relevant substrate(s) in photoreceptors unidentified","Mechanism linking DUB activity to photoreceptor maintenance unknown"]},{"year":2023,"claim":"Implicated USP45 in oncogenesis by showing it stabilizes MYC to drive stemness and drug resistance, and identified a small-molecule inhibitor.","evidence":"Co-IP/GST pulldown, in vitro deubiquitination, overexpression/knockdown, MYC epistasis, xenograft, α-mangostin binding","pmids":["36765885"],"confidence":"Medium","gaps":["Ubiquitin linkage on MYC not defined","Inhibitor selectivity beyond reported binding not fully characterized"]},{"year":2023,"claim":"Defined a recruitment mechanism for USP45 onto a substrate, showing MYH9/MYH10 deliver USP45 to deubiquitylate and stabilize Snail, promoting EMT and chemoresistance.","evidence":"Co-IP, GST pulldown, confocal co-localization, MYH10 knockdown in vitro/in vivo, epistasis","pmids":["36929633"],"confidence":"Medium","gaps":["Direct vs adaptor-mediated USP45-Snail contact not separated","Generality of myosin-mediated recruitment to other substrates unknown"]},{"year":2025,"claim":"Linked USP45 to lysosomal and autophagy regulation via Coronin 1B, establishing an actin/V-ATPase mechanistic axis conserved across species.","evidence":"Co-IP, in vitro deubiquitination, KO/KD, F-actin and V-ATPase imaging, lysosomal acidification and autophagy flux assays in Drosophila and mammalian cells","pmids":["40067150"],"confidence":"High","gaps":["Ubiquitin linkage type on Coro1B not specified","How USP45 activity is regulated in this pathway unknown"]},{"year":2025,"claim":"Revealed an asymmetric multi-substrate regulatory hierarchy in which USP45 stabilizes RTCB and DDX1, with DDX1 deubiquitination requiring RTCB.","evidence":"Co-IP, co-localization, in vitro deubiquitination, RTCB/DDX1 knockdown epistasis, xenograft","pmids":["41468936"],"confidence":"Medium","gaps":["Structural basis of the RTCB-dependent hierarchy unresolved","Single-lab finding"]},{"year":2025,"claim":"Identified a tumor-suppressive context for USP45, showing its catalytic domain binds and stabilizes MRGPRF by removing K63 chains to inhibit melanoma malignancy.","evidence":"Screen of 40 USPs, Co-IP, in vitro deubiquitination with K63 specificity, domain mapping, MRGPRF KD/OE epistasis, xenograft","pmids":["40788071"],"confidence":"Medium","gaps":["Reconciliation of pro- and anti-tumor roles across cancer types not addressed","Upstream control of USP45 in melanoma unknown"]},{"year":2026,"claim":"Extended USP45 into antiviral innate immunity, showing it is interferon-induced and deubiquitylates HIV-1 Tat at K19 to suppress viral transcription.","evidence":"NanoBRET DUB screen, Co-IP, site-specific (K19) in vitro deubiquitination, transcription and viral production assays, digital PCR in latent cells, interferon stimulation","pmids":["41668887"],"confidence":"Medium","gaps":["Effect of Tat deubiquitination on Tat function mechanistically incomplete","In vivo antiviral relevance not tested"]},{"year":null,"claim":"How USP45 selects among its many substrates and switches linkage preferences (K48/K63/K6) in different cellular contexts, and how its activity is regulated, remain unresolved.","evidence":"No single study integrates substrate selection, linkage choice, and activity regulation","pmids":[],"confidence":"Low","gaps":["No structural model of substrate engagement","Determinants of linkage specificity unknown","Regulation of USP45 catalytic activity uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,4,5,6,7,8,9]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,6,9]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[6]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,4,5,6,7,8]}],"complexes":[],"partners":["ERCC1","SPDL1","MYC","SNAI1","CORO1B","RTCB","DDX1","MRGPRF"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q70EL2","full_name":"Ubiquitin carboxyl-terminal hydrolase 45","aliases":["Deubiquitinating enzyme 45","Ubiquitin thioesterase 45","Ubiquitin-specific-processing protease 45"],"length_aa":814,"mass_kda":91.7,"function":"Catalyzes the deubiquitination of SPDL1 (PubMed:30258100). Plays a role in the repair of UV-induced DNA damage via deubiquitination of ERCC1, promoting its recruitment to DNA damage sites (PubMed:25538220). May be involved in the maintenance of photoreceptor function (PubMed:30573563). May play a role in normal retinal development (By similarity). Plays a role in cell migration (PubMed:30258100)","subcellular_location":"Photoreceptor inner segment; Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q70EL2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/USP45","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":[{"gene":"CSNK2B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/USP45","total_profiled":1310},"omim":[{"mim_id":"618513","title":"LEBER CONGENITAL AMAUROSIS 19; LCA19","url":"https://www.omim.org/entry/618513"},{"mim_id":"618439","title":"UBIQUITIN-SPECIFIC PROTEASE 45; USP45","url":"https://www.omim.org/entry/618439"},{"mim_id":"609101","title":"F-BOX ONLY PROTEIN 30; FBXO30","url":"https://www.omim.org/entry/609101"},{"mim_id":"204000","title":"LEBER CONGENITAL AMAUROSIS 1; LCA1","url":"https://www.omim.org/entry/204000"},{"mim_id":"126380","title":"ERCC EXCISION REPAIR 1, ENDONUCLEASE NONCATALYTIC SUBUNIT; ERCC1","url":"https://www.omim.org/entry/126380"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/USP45"},"hgnc":{"alias_symbol":["MGC14793"],"prev_symbol":[]},"alphafold":{"accession":"Q70EL2","domains":[{"cath_id":"3.30.40.10","chopping":"40-171","consensus_level":"high","plddt":74.7925,"start":40,"end":171},{"cath_id":"-","chopping":"199-351","consensus_level":"high","plddt":83.1116,"start":199,"end":351},{"cath_id":"3.90.70.10","chopping":"356-386_601-655_665-762_781-813","consensus_level":"medium","plddt":87.4424,"start":356,"end":813}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q70EL2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q70EL2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q70EL2-F1-predicted_aligned_error_v6.png","plddt_mean":65.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=USP45","jax_strain_url":"https://www.jax.org/strain/search?query=USP45"},"sequence":{"accession":"Q70EL2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q70EL2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q70EL2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q70EL2"}},"corpus_meta":[{"pmid":"2123812","id":"PMC_2123812","title":"Cloning of usp45, a gene encoding a secreted protein from Lactococcus lactis subsp. lactis MG1363.","date":"1990","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/2123812","citation_count":185,"is_preprint":false},{"pmid":"8413193","id":"PMC_8413193","title":"Functional analysis of the Lactococcus lactis usp45 secretion signal in the secretion of a homologous proteinase and a heterologous alpha-amylase.","date":"1993","source":"Molecular & general genetics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/8413193","citation_count":76,"is_preprint":false},{"pmid":"25538220","id":"PMC_25538220","title":"USP45 deubiquitylase controls ERCC1-XPF endonuclease-mediated DNA damage responses.","date":"2014","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/25538220","citation_count":51,"is_preprint":false},{"pmid":"20842358","id":"PMC_20842358","title":"Use of the usp45 lactococcal secretion signal sequence to drive the secretion and functional expression of enterococcal bacteriocins in Lactococcus lactis.","date":"2010","source":"Applied microbiology and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/20842358","citation_count":32,"is_preprint":false},{"pmid":"36929633","id":"PMC_36929633","title":"MYH10 Combines with MYH9 to Recruit USP45 by Deubiquitinating Snail and Promotes Serous Ovarian Cancer Carcinogenesis, Progression, and Cisplatin Resistance.","date":"2023","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/36929633","citation_count":28,"is_preprint":false},{"pmid":"30573563","id":"PMC_30573563","title":"Biallelic mutations in USP45, encoding a deubiquitinating enzyme, are associated with Leber congenital amaurosis.","date":"2018","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30573563","citation_count":19,"is_preprint":false},{"pmid":"30258100","id":"PMC_30258100","title":"USP45 and Spindly are part of the same complex implicated in cell migration.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30258100","citation_count":15,"is_preprint":false},{"pmid":"36765885","id":"PMC_36765885","title":"Suppression of Cancer Cell Stemness and Drug Resistance via MYC Destabilization by Deubiquitinase USP45 Inhibition with a Natural Small Molecule.","date":"2023","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/36765885","citation_count":15,"is_preprint":false},{"pmid":"27613029","id":"PMC_27613029","title":"Combining Zebrafish and Mouse Models to Test the Function of Deubiquitinating Enzyme (Dubs) Genes in Development: Role of USP45 in the Retina.","date":"2016","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/27613029","citation_count":15,"is_preprint":false},{"pmid":"32532874","id":"PMC_32532874","title":"Another Breaker of the Wall: the Biological Function of the Usp45 Protein of Lactococcus lactis.","date":"2020","source":"Applied and environmental microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/32532874","citation_count":14,"is_preprint":false},{"pmid":"35836933","id":"PMC_35836933","title":"Comprehensive Analysis Reveals USP45 as a Novel Putative Oncogene in Pan-Cancer.","date":"2022","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/35836933","citation_count":11,"is_preprint":false},{"pmid":"32335791","id":"PMC_32335791","title":"Secretion of recombinant xylanase in Lactococcus lactis using signal peptides Usp45 and Spk1.","date":"2020","source":"Biotechnology letters","url":"https://pubmed.ncbi.nlm.nih.gov/32335791","citation_count":7,"is_preprint":false},{"pmid":"40788071","id":"PMC_40788071","title":"USP45 Represses Melanoma Development by Deubiquitinating and Stabilizing Tumor Suppressor MRGPRF.","date":"2025","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/40788071","citation_count":3,"is_preprint":false},{"pmid":"40067150","id":"PMC_40067150","title":"The deubiquitinase USP45 inhibits autophagy through actin regulation by Coronin 1B.","date":"2025","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/40067150","citation_count":3,"is_preprint":false},{"pmid":"41468936","id":"PMC_41468936","title":"Deubiquitinase USP45 stabilizes RTCB and DDX1, promoting tumorigenesis and chemoresistance.","date":"2025","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/41468936","citation_count":1,"is_preprint":false},{"pmid":"38581868","id":"PMC_38581868","title":"Production of recombinant glycosidases fused with Usp45 and SpaX to avoid the purification and immobilization stages.","date":"2024","source":"Enzyme and microbial technology","url":"https://pubmed.ncbi.nlm.nih.gov/38581868","citation_count":0,"is_preprint":false},{"pmid":"41668887","id":"PMC_41668887","title":"USP45-mediated deubiquitination of HIV-1 Tat regulates viral transcription and latency.","date":"2026","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/41668887","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.27.25333852","title":"Ultrarare Variants in DNA Damage Repair and Mitochondrial Genes in Pediatric Acute-Onset Neuropsychiatric Syndrome and Acute Behavioral Regression in Neurodevelopmental Disorders","date":"2025-08-27","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.27.25333852","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10854,"output_tokens":3021,"usd":0.038939,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10301,"output_tokens":3398,"usd":0.068227,"stage2_stop_reason":"end_turn"},"total_usd":0.107166,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"USP45 associates with ERCC1 (a subunit of the XPF-ERCC1 DNA repair endonuclease) via a short acidic motif outside the USP45 catalytic domain, and directly deubiquitylates ERCC1 in vitro. USP45 knockout cells show markedly elevated ubiquitylated ERCC1 and are hypersensitive to UV irradiation and DNA interstrand cross-links, similar to ERCC1-deficient cells. ERCC1 translocation to DNA damage-induced subnuclear foci is impaired in USP45 knockout cells. USP45 itself localizes to sites of DNA damage in a manner dependent on its deubiquitylase activity but independent of ERCC1-XPF binding.\",\n      \"method\": \"In vitro deubiquitylation assay, Co-IP, mutant analysis (catalytic-dead and ERCC1-binding-deficient USP45), knockout cell lines, UV/ICL sensitivity assays, immunofluorescence of subnuclear foci\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro deubiquitylation assay with mutagenesis, reciprocal binding studies, KO cells with multiple orthogonal phenotypic readouts in a single rigorous study\",\n      \"pmids\": [\"25538220\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"USP45 forms a complex with Spindly (identified by mass spectrometry), and this interaction depends on the catalytic activity of USP45. USP45 preferentially cleaves K48-linked ubiquitin chains and potentially K6-linked chains. Spindly is mono-ubiquitylated, and this modification is specifically removed by catalytically active but not catalytic-inactive USP45. Loss of USP45 impairs cell migration, similar to loss of Spindly.\",\n      \"method\": \"Mass spectrometry-based interactome, Co-IP, in vitro deubiquitylation assay with catalytic-dead mutant, cell migration assay (knockdown)\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — MS identification plus Co-IP and in vitro activity assay, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"30258100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Morpholino-mediated knockdown of usp45 in zebrafish causes abnormal retinal development with defective formation of retinal structures, establishing a functional role for USP45 in vertebrate retina differentiation.\",\n      \"method\": \"Morpholino knockdown in zebrafish embryos, phenotypic analysis of retinal morphology\",\n      \"journal\": \"Methods in molecular biology (Clifton, N.J.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — zebrafish KD with defined cellular phenotype; single lab, single model organism\",\n      \"pmids\": [\"27613029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Biallelic loss-of-function mutations in USP45 cause Leber congenital amaurosis. USP45 protein is enriched in the inner segments of photoreceptors (human and zebrafish retina). usp45 morpholino knockdown in zebrafish causes abnormal retinal development rescued by wild-type usp45 mRNA. Targeted knockout of Usp45 in mice produces abnormal electroretinography responses consistent with LCA.\",\n      \"method\": \"Whole-exome sequencing, immunohistochemistry for localization, zebrafish morpholino knockdown with mRNA rescue, mouse knockout with ERG functional readout\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal models (zebrafish KD with rescue, mouse KO with functional ERG), localization by IHC, replication of retinal phenotype across two species\",\n      \"pmids\": [\"30573563\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"USP45 directly binds MYC and deubiquitinates/stabilizes it, preventing its proteasomal degradation. USP45 overexpression upregulates MYC and enhances cancer cell stemness and drug resistance. The natural small molecule α-mangostin specifically binds and inhibits USP45, suppressing USP45-induced stemness and drug resistance in vitro and in a cervical cancer xenograft model.\",\n      \"method\": \"Co-IP/GST pulldown, in vitro deubiquitination assay, USP45 overexpression/shRNA knockdown, MYC shRNA epistasis, xenograft mouse model, binding assay with α-mangostin\",\n      \"journal\": \"Cancers\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct binding and in vitro deubiquitination assay reported, epistasis with MYC shRNA, single lab\",\n      \"pmids\": [\"36765885\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MYH10 combines with MYH9 to recruit USP45, which then deubiquitinates Snail, preventing its degradation and promoting EMT, tumorigenesis, and cisplatin resistance in serous ovarian cancer. Interaction was established by Co-IP and GST pulldown.\",\n      \"method\": \"Co-IP, GST pulldown, confocal co-localization, knockdown of MYH10 in vitro and in vivo, MYH10/MYH9/Snail epistasis\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP and GST pulldown for interaction, single lab, in vivo xenograft confirmation of phenotype\",\n      \"pmids\": [\"36929633\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"USP45 interacts with and deubiquitinates Coronin 1B (Coro1B), stabilizing Coro1B protein levels. Loss of USP45 or Coro1B promotes formation of F-actin patches and translocation of V-ATPase to lysosomes in an N-WASP-dependent manner, leading to increased lysosomal acidification, enhanced lysosomal function, and autophagy activation. This pathway was demonstrated in both Drosophila and mammalian cells.\",\n      \"method\": \"Co-IP, in vitro deubiquitination assay, USP45/Coro1B KO/KD, F-actin imaging, V-ATPase localization assay, lysosomal acidification assay, autophagy flux assay in Drosophila and mammalian cells\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — Co-IP plus in vitro deubiquitination, genetic epistasis (N-WASP dependence), multiple orthogonal readouts, replicated across two model systems\",\n      \"pmids\": [\"40067150\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"USP45 directly interacts with and deubiquitinates both RTCB and DDX1, removing polyubiquitin chains and stabilizing these proteins. USP45-mediated DDX1 deubiquitination requires RTCB (asymmetric regulatory hierarchy), whereas RTCB deubiquitination is DDX1-independent. This USP45-RTCB-DDX1 axis promotes cell proliferation and chemoresistance in cellular and murine models.\",\n      \"method\": \"Co-IP, co-localization, in vitro deubiquitination assay, epistasis using RTCB/DDX1 knockdown, xenograft mouse model\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct in vitro deubiquitination and Co-IP reported, asymmetric epistasis established, single lab\",\n      \"pmids\": [\"41468936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"USP45's catalytic domain directly binds the N-terminus of MRGPRF and stabilizes MRGPRF, specifically by removing K63-linked ubiquitination from MRGPRF in melanoma cells. USP45 overexpression inhibits melanoma cell malignancy via MRGPRF, and MRGPRF depletion mitigates USP45's anti-melanoma effects; MRGPRF overexpression rescues the enhanced malignancy caused by USP45 deficiency.\",\n      \"method\": \"Screening of 40 USPs, Co-IP, in vitro deubiquitination assay (K63-chain specificity), domain mapping, epistasis via MRGPRF KD/OE, xenograft mouse model\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — in vitro deubiquitination with chain-type specificity, genetic epistasis, single lab\",\n      \"pmids\": [\"40788071\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"USP45 specifically deubiquitinates HIV-1 Tat at lysine 19, targeting both K48-linked and K63-linked ubiquitin chains. USP45 overexpression suppresses Tat-dependent HIV-1 transcriptional activation and viral particle production, while USP45 knockdown enhances both. USP45 primarily inhibits the initial stages of viral transcription in latently infected cells. USP45 expression is induced by interferons, identifying it as an interferon-stimulated gene.\",\n      \"method\": \"NanoBRET-based DUB screening, Co-IP, in vitro deubiquitination assay with site-specific mapping (K19), USP45 overexpression/knockdown, HIV-1 transcription assay, digital PCR in latently infected cells, interferon stimulation\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — site-specific deubiquitination mapping and functional transcription assay, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"41668887\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"USP45 is a catalytically active deubiquitylase (DUB) that stabilizes multiple substrates—including ERCC1, Spindly, MYC, Snail, Coronin 1B, MRGPRF, RTCB, DDX1, and HIV-1 Tat—by removing ubiquitin chains (with preferences for K48, K63, or K6 linkages depending on substrate), thereby regulating DNA damage repair (via XPF-ERCC1 recruitment to damage foci), autophagy and lysosomal function (via Coronin 1B/actin/V-ATPase axis), cell migration (via Spindly), retinal photoreceptor maintenance, and oncogenic pathways including EMT (Snail), stemness (MYC), and anti-melanoma signaling (MRGPRF).\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"USP45 is a catalytically active deubiquitylase that controls the stability and localization of diverse substrates by removing ubiquitin chains, with linkage preferences (K48, K63, K6) that vary by target [#0, #1, #8]. In genome maintenance, USP45 associates with ERCC1 through an acidic motif outside its catalytic domain and directly deubiquitylates ERCC1; loss of USP45 elevates ubiquitylated ERCC1, impairs ERCC1 recruitment to DNA damage foci, and sensitizes cells to UV and interstrand cross-links, while USP45 itself localizes to damage sites in an activity-dependent manner [#0]. Biallelic loss-of-function mutations in USP45 cause Leber congenital amaurosis, consistent with its enrichment in photoreceptor inner segments and the retinal phenotypes produced by zebrafish knockdown (rescued by wild-type mRNA) and mouse knockout [#3]. Beyond these roles, USP45 acts broadly as a substrate-stabilizing DUB: it deubiquitylates Coronin 1B to restrain F-actin/V-ATPase-driven lysosomal acidification and autophagy [#6], stabilizes Spindly to support cell migration [#1], and stabilizes oncogenic and signaling substrates including MYC, Snail, the RTCB-DDX1 axis, and MRGPRF, and removes ubiquitin from HIV-1 Tat as an interferon-stimulated gene [#4, #5, #7, #8, #9].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established USP45 as a bona fide deubiquitylase with a defined substrate (ERCC1) and a concrete role in nucleotide excision/cross-link repair, answering whether USP45 has enzymatic function and a biological context.\",\n      \"evidence\": \"In vitro deubiquitylation, Co-IP, catalytic-dead and binding-deficient mutants, knockout cells with UV/ICL sensitivity and foci imaging\",\n      \"pmids\": [\"25538220\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Linkage specificity of ERCC1 chains not defined\", \"Mechanism of USP45 recruitment to damage sites independent of ERCC1-XPF unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Provided the first in vivo developmental role for USP45, showing it is required for vertebrate retinal differentiation.\",\n      \"evidence\": \"Morpholino knockdown in zebrafish with retinal morphology analysis\",\n      \"pmids\": [\"27613029\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular substrate linked to the retinal phenotype\", \"Morpholino specificity not controlled by rescue in this report\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Connected USP45 to cytoskeletal/migration biology by identifying Spindly as a catalytic-activity-dependent substrate and defining linkage preference (K48, possibly K6).\",\n      \"evidence\": \"Mass spectrometry interactome, Co-IP, in vitro deubiquitylation with catalytic-dead mutant, migration assay on knockdown\",\n      \"pmids\": [\"30258100\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of Spindly mono-ubiquitin removal on its known roles not mapped\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established USP45 as a human disease gene, demonstrating that biallelic loss-of-function causes Leber congenital amaurosis with cross-species replication.\",\n      \"evidence\": \"Whole-exome sequencing, IHC localization, zebrafish knockdown with mRNA rescue, mouse knockout with ERG\",\n      \"pmids\": [\"30573563\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relevant substrate(s) in photoreceptors unidentified\", \"Mechanism linking DUB activity to photoreceptor maintenance unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Implicated USP45 in oncogenesis by showing it stabilizes MYC to drive stemness and drug resistance, and identified a small-molecule inhibitor.\",\n      \"evidence\": \"Co-IP/GST pulldown, in vitro deubiquitination, overexpression/knockdown, MYC epistasis, xenograft, α-mangostin binding\",\n      \"pmids\": [\"36765885\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin linkage on MYC not defined\", \"Inhibitor selectivity beyond reported binding not fully characterized\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined a recruitment mechanism for USP45 onto a substrate, showing MYH9/MYH10 deliver USP45 to deubiquitylate and stabilize Snail, promoting EMT and chemoresistance.\",\n      \"evidence\": \"Co-IP, GST pulldown, confocal co-localization, MYH10 knockdown in vitro/in vivo, epistasis\",\n      \"pmids\": [\"36929633\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs adaptor-mediated USP45-Snail contact not separated\", \"Generality of myosin-mediated recruitment to other substrates unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linked USP45 to lysosomal and autophagy regulation via Coronin 1B, establishing an actin/V-ATPase mechanistic axis conserved across species.\",\n      \"evidence\": \"Co-IP, in vitro deubiquitination, KO/KD, F-actin and V-ATPase imaging, lysosomal acidification and autophagy flux assays in Drosophila and mammalian cells\",\n      \"pmids\": [\"40067150\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin linkage type on Coro1B not specified\", \"How USP45 activity is regulated in this pathway unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed an asymmetric multi-substrate regulatory hierarchy in which USP45 stabilizes RTCB and DDX1, with DDX1 deubiquitination requiring RTCB.\",\n      \"evidence\": \"Co-IP, co-localization, in vitro deubiquitination, RTCB/DDX1 knockdown epistasis, xenograft\",\n      \"pmids\": [\"41468936\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of the RTCB-dependent hierarchy unresolved\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a tumor-suppressive context for USP45, showing its catalytic domain binds and stabilizes MRGPRF by removing K63 chains to inhibit melanoma malignancy.\",\n      \"evidence\": \"Screen of 40 USPs, Co-IP, in vitro deubiquitination with K63 specificity, domain mapping, MRGPRF KD/OE epistasis, xenograft\",\n      \"pmids\": [\"40788071\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reconciliation of pro- and anti-tumor roles across cancer types not addressed\", \"Upstream control of USP45 in melanoma unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Extended USP45 into antiviral innate immunity, showing it is interferon-induced and deubiquitylates HIV-1 Tat at K19 to suppress viral transcription.\",\n      \"evidence\": \"NanoBRET DUB screen, Co-IP, site-specific (K19) in vitro deubiquitination, transcription and viral production assays, digital PCR in latent cells, interferon stimulation\",\n      \"pmids\": [\"41668887\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Effect of Tat deubiquitination on Tat function mechanistically incomplete\", \"In vivo antiviral relevance not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How USP45 selects among its many substrates and switches linkage preferences (K48/K63/K6) in different cellular contexts, and how its activity is regulated, remain unresolved.\",\n      \"evidence\": \"No single study integrates substrate selection, linkage choice, and activity regulation\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of substrate engagement\", \"Determinants of linkage specificity unknown\", \"Regulation of USP45 catalytic activity uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 4, 5, 6, 7, 8, 9]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 6, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 4, 5, 6, 7, 8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"ERCC1\", \"SPDL1\", \"MYC\", \"SNAI1\", \"CORO1B\", \"RTCB\", \"DDX1\", \"MRGPRF\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}