{"gene":"CTU2","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2019,"finding":"CTU2 forms a complex with CTU1 that catalyzes thiolation of the wobble uridine (U34) in tRNA anticodon loops; biallelic loss-of-function variants in CTU2 in patient-derived cells specifically impair 2-thiolation of all wobble uridine-containing tRNAs (tRNA-Lys, tRNA-Gln, tRNA-Glu).","method":"Functional characterization of patient-derived cells carrying five different CTU2 alleles (including protein-truncating variants); wobble uridine thiolation assessed biochemically in human cells","journal":"Human mutation","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple patient alleles tested in patient-derived cells with direct biochemical readout, replicated across five independent alleles in a single rigorous study","pmids":["31301155"],"is_preprint":false},{"year":2023,"finding":"The Ncs2 (CTU2 ortholog in yeast) protein is essential for 2-thiolation of tRNA at the wobble uridine; a gain-of-function point mutation (NCS2*) identified in a clinical isolate increases thiolation efficiency at elevated temperature, alters the interaction and stability of the thiolase complex likely through nucleotide binding, and loss of 2-thiolation abrogates in vivo virulence of pathogenic yeast.","method":"Genetic characterization of NCS2* point mutant; biochemical analysis of tRNA thiolation levels; complex stability and interaction assays; mouse infection model and Candida albicans cell culture virulence model","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (biochemical thiolation assay, complex interaction/stability assay, in vivo infection model, morphology assays) in a single study with clear mechanistic readouts","pmids":["37462076"],"is_preprint":false},{"year":2024,"finding":"CTU2 expression is transcriptionally activated by Liver X Receptor (LXR) through a canonical LXR response element in the CTU2 promoter; CTU2 promotes lipogenesis by enhancing synthesis of lipogenic proteins, and its knockdown reduces tumor burden and synergizes with LXR ligands to induce apoptosis and inhibit proliferation in hepatocellular carcinoma cells and xenograft models.","method":"LXR agonist treatment and LXR knockout in HepG2 cells; xenograft nude mouse model; promoter analysis identifying LXR response element; CTU2 knockdown with proliferation and apoptosis readouts","journal":"Cell biology and toxicology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — LXR-CTU2 transcriptional regulation shown by agonist/KO plus promoter element, and lipogenesis/tumor role shown by KD in vitro and in vivo, but mechanistic detail on how CTU2 enhances lipogenic protein synthesis is not fully resolved in abstract","pmids":["38630355"],"is_preprint":false},{"year":2025,"finding":"USF1 is identified as a transcription factor that regulates CTU2 expression; CTU2 overexpression in tumors is associated with DNA copy number amplification and DNA methylation alterations; CTU2 modifies tRNA-Lys-TTT at the wobble position.","method":"ChIP-seq data analysis, dual-luciferase reporter assay, EMSA for USF1 binding to CTU2 promoter; genomic copy number and methylation analysis from pan-cancer datasets; in vitro and in vivo oncogenic validation","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — USF1 regulation supported by dual-luciferase and EMSA (two orthogonal methods), single lab, no replication","pmids":["40375999"],"is_preprint":false}],"current_model":"CTU2 (also known as NCS2/C16orf84) is an essential subunit of the conserved CTU1/CTU2 complex that catalyzes 2-thiolation of the wobble uridine (U34) in cytoplasmic tRNAs (tRNA-Lys, tRNA-Gln, tRNA-Glu); loss-of-function causes DREAM-PL syndrome in humans via global impairment of wobble uridine thiolation, while its expression is transcriptionally regulated by LXR (through a promoter LXR response element) and USF1, and it additionally promotes lipogenesis and tumor progression in hepatocellular carcinoma."},"narrative":{"mechanistic_narrative":"CTU2 is an essential subunit of the cytoplasmic CTU1/CTU2 thiolase complex that catalyzes 2-thiolation of the wobble uridine (U34) in the anticodon loop of tRNA-Lys, tRNA-Gln, and tRNA-Glu, a modification required for accurate decoding [PMID:31301155]. In patient-derived cells, biallelic loss-of-function variants in CTU2 specifically abolish 2-thiolation across all wobble uridine-containing tRNAs, establishing the protein's catalytic indispensability and linking its loss to a human Mendelian disorder [PMID:31301155]. The requirement of the CTU2 ortholog (Ncs2) for wobble uridine thiolation is conserved in yeast, where loss of 2-thiolation abrogates pathogenic virulence and complex stability and interaction depend on nucleotide binding [PMID:37462076]. Beyond its tRNA-modifying role, CTU2 expression is transcriptionally activated by Liver X Receptor through a promoter LXR response element and by USF1, and CTU2 promotes lipogenesis and tumor progression in hepatocellular carcinoma, where its knockdown reduces tumor burden and synergizes with LXR ligands to induce apoptosis [PMID:38630355, PMID:40375999].","teleology":[{"year":2019,"claim":"Established that CTU2 is the catalytic determinant of wobble uridine 2-thiolation in human tRNAs and that its loss causes a defined biochemical and clinical phenotype.","evidence":"Functional characterization of patient-derived cells carrying five CTU2 alleles with direct biochemical thiolation readout","pmids":["31301155"],"confidence":"High","gaps":["Structural basis of the CTU1/CTU2 catalytic mechanism not resolved","Downstream translational consequences of thiolation loss not directly mapped","Stoichiometry and assembly of the complex in human cells not defined"]},{"year":2023,"claim":"Showed the thiolation function is evolutionarily conserved and physiologically consequential, with complex stability dependent on nucleotide binding and thiolation required for fungal virulence.","evidence":"Genetic and biochemical analysis of NCS2* point mutant, complex interaction/stability assays, and mouse and Candida albicans virulence models","pmids":["37462076"],"confidence":"High","gaps":["Direct extrapolation of yeast findings to human CTU2 not established","Nucleotide-binding site within the complex not structurally defined"]},{"year":2024,"claim":"Linked CTU2 to lipid metabolism and cancer by identifying LXR-driven transcriptional control and a pro-lipogenic, pro-tumorigenic role in hepatocellular carcinoma.","evidence":"LXR agonist/knockout in HepG2 cells, promoter LXR response element analysis, CTU2 knockdown, and xenograft mouse model","pmids":["38630355"],"confidence":"Medium","gaps":["Mechanism by which CTU2 enhances lipogenic protein synthesis not resolved","Whether tumor effects depend on tRNA thiolation activity is untested"]},{"year":2025,"claim":"Extended transcriptional regulation to USF1 and connected CTU2 overexpression to genomic and epigenetic alterations in cancer while confirming tRNA-Lys-TTT modification.","evidence":"ChIP-seq analysis, dual-luciferase reporter, EMSA for USF1 binding, pan-cancer copy number and methylation analysis, and oncogenic validation","pmids":["40375999"],"confidence":"Medium","gaps":["Single-lab USF1 regulation without independent replication","Causal link between copy number/methylation changes and CTU2 expression not established"]},{"year":null,"claim":"How CTU2-dependent wobble uridine thiolation mechanistically couples to lipogenesis and tumor progression remains unresolved.","evidence":"No timeline discovery directly tests whether the oncogenic/lipogenic functions require catalytic thiolation activity","pmids":[],"confidence":"Medium","gaps":["No structural model of the human CTU1/CTU2 complex","Translational targets affected by thiolation loss not enumerated","Whether metabolic and disease roles are catalysis-dependent is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2]}],"complexes":["CTU1/CTU2 thiolase complex"],"partners":["CTU1","LXR","USF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q2VPK5","full_name":"Cytoplasmic tRNA 2-thiolation protein 2","aliases":["Cytosolic thiouridylase subunit 2"],"length_aa":515,"mass_kda":56.1,"function":"Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). May act by forming a heterodimer with CTU1/ATPBD3 that ligates sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q2VPK5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CTU2","classification":"Common Essential","n_dependent_lines":968,"n_total_lines":1208,"dependency_fraction":0.8013245033112583},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CTU2","total_profiled":1310},"omim":[{"mim_id":"618142","title":"MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME; MFRG","url":"https://www.omim.org/entry/618142"},{"mim_id":"617057","title":"CYTOSOLIC THIOURIDYLASE, SUBUNIT 2; CTU2","url":"https://www.omim.org/entry/617057"},{"mim_id":"612722","title":"ELONGATOR ACETYLTRANSFERASE COMPLEX, SUBUNIT 3; ELP3","url":"https://www.omim.org/entry/612722"},{"mim_id":"612694","title":"CYTOSOLIC THIOURIDYLASE, SUBUNIT 1; CTU1","url":"https://www.omim.org/entry/612694"},{"mim_id":"164757","title":"B-RAF PROTOONCOGENE, SERINE/THREONINE KINASE; BRAF","url":"https://www.omim.org/entry/164757"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mitochondria","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CTU2"},"hgnc":{"alias_symbol":["NCS2"],"prev_symbol":["C16orf84"]},"alphafold":{"accession":"Q2VPK5","domains":[{"cath_id":"-","chopping":"22-68","consensus_level":"medium","plddt":90.6021,"start":22,"end":68},{"cath_id":"3.40.50.620","chopping":"70-165_213-370","consensus_level":"high","plddt":93.6863,"start":70,"end":370}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q2VPK5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q2VPK5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q2VPK5-F1-predicted_aligned_error_v6.png","plddt_mean":79.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CTU2","jax_strain_url":"https://www.jax.org/strain/search?query=CTU2"},"sequence":{"accession":"Q2VPK5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q2VPK5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q2VPK5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q2VPK5"}},"corpus_meta":[{"pmid":"7851780","id":"PMC_7851780","title":"The maize NCS2 abnormal growth mutant has a chimeric nad4-nad7 mitochondrial gene and is associated with reduced complex I function.","date":"1994","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/7851780","citation_count":85,"is_preprint":false},{"pmid":"31301155","id":"PMC_31301155","title":"Biallelic variants in CTU2 cause DREAM-PL syndrome and impair thiolation of tRNA wobble U34.","date":"2019","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/31301155","citation_count":23,"is_preprint":false},{"pmid":"29437264","id":"PMC_29437264","title":"Insight on specificity of uracil permeases of the NAT/NCS2 family from analysis of the transporter encoded in the pyrimidine utilization operon of Escherichia coli.","date":"2018","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/29437264","citation_count":17,"is_preprint":false},{"pmid":"24169576","id":"PMC_24169576","title":"A critical role for the putative NCS2 nucleobase permease YjcD in the sensitivity of Escherichia coli to cytotoxic and mutagenic purine analogs.","date":"2013","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/24169576","citation_count":14,"is_preprint":false},{"pmid":"25639910","id":"PMC_25639910","title":"Functional characterization of NAT/NCS2 proteins of Aspergillus brasiliensis reveals a genuine xanthine-uric acid transporter and an intrinsically misfolded polypeptide.","date":"2015","source":"Fungal genetics and biology : FG & B","url":"https://pubmed.ncbi.nlm.nih.gov/25639910","citation_count":13,"is_preprint":false},{"pmid":"30418564","id":"PMC_30418564","title":"NAT/NCS2-hound: a webserver for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family.","date":"2018","source":"GigaScience","url":"https://pubmed.ncbi.nlm.nih.gov/30418564","citation_count":11,"is_preprint":false},{"pmid":"11937090","id":"PMC_11937090","title":"The effect of a Titanocene Dichloride derivative, Ti IV (C5H5)(2) NCS(2), on the haematopoietic response of Ehrlich tumour-bearing mice.","date":"2002","source":"European journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/11937090","citation_count":11,"is_preprint":false},{"pmid":"37462076","id":"PMC_37462076","title":"Ncs2* mediates in vivo virulence of pathogenic yeast through sulphur modification of cytoplasmic transfer RNA.","date":"2023","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/37462076","citation_count":8,"is_preprint":false},{"pmid":"9428593","id":"PMC_9428593","title":"Rhenium-188 and technetium-99m nitridobis(N-ethoxy-N-ethyldithiocarbamate) leucocyte labelling radiopharmaceuticals: [188ReN(NOET)2] and [99mTcN(NOET)2], NOET = Et(EtO)NCS2: their in vitro localization and chemical behaviour.","date":"1997","source":"Nuclear medicine and biology","url":"https://pubmed.ncbi.nlm.nih.gov/9428593","citation_count":8,"is_preprint":false},{"pmid":"38630355","id":"PMC_38630355","title":"Activation of CTU2 expression by LXR promotes the development of hepatocellular carcinoma.","date":"2024","source":"Cell biology and toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/38630355","citation_count":4,"is_preprint":false},{"pmid":"39475230","id":"PMC_39475230","title":"Substrate identification of putative NCS1 and NCS2 nucleobase transporters in Pseudomonas aeruginosa.","date":"2024","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/39475230","citation_count":1,"is_preprint":false},{"pmid":"40375999","id":"PMC_40375999","title":"Pan-cancer analysis identifies tRNA modification enzyme CTU2 as a novel tumor biomarker and its role in immune microenvironment.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/40375999","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8275,"output_tokens":1278,"usd":0.021997,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7890,"output_tokens":1948,"usd":0.044075,"stage2_stop_reason":"end_turn"},"total_usd":0.066072,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"CTU2 forms a complex with CTU1 that catalyzes thiolation of the wobble uridine (U34) in tRNA anticodon loops; biallelic loss-of-function variants in CTU2 in patient-derived cells specifically impair 2-thiolation of all wobble uridine-containing tRNAs (tRNA-Lys, tRNA-Gln, tRNA-Glu).\",\n      \"method\": \"Functional characterization of patient-derived cells carrying five different CTU2 alleles (including protein-truncating variants); wobble uridine thiolation assessed biochemically in human cells\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple patient alleles tested in patient-derived cells with direct biochemical readout, replicated across five independent alleles in a single rigorous study\",\n      \"pmids\": [\"31301155\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The Ncs2 (CTU2 ortholog in yeast) protein is essential for 2-thiolation of tRNA at the wobble uridine; a gain-of-function point mutation (NCS2*) identified in a clinical isolate increases thiolation efficiency at elevated temperature, alters the interaction and stability of the thiolase complex likely through nucleotide binding, and loss of 2-thiolation abrogates in vivo virulence of pathogenic yeast.\",\n      \"method\": \"Genetic characterization of NCS2* point mutant; biochemical analysis of tRNA thiolation levels; complex stability and interaction assays; mouse infection model and Candida albicans cell culture virulence model\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (biochemical thiolation assay, complex interaction/stability assay, in vivo infection model, morphology assays) in a single study with clear mechanistic readouts\",\n      \"pmids\": [\"37462076\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CTU2 expression is transcriptionally activated by Liver X Receptor (LXR) through a canonical LXR response element in the CTU2 promoter; CTU2 promotes lipogenesis by enhancing synthesis of lipogenic proteins, and its knockdown reduces tumor burden and synergizes with LXR ligands to induce apoptosis and inhibit proliferation in hepatocellular carcinoma cells and xenograft models.\",\n      \"method\": \"LXR agonist treatment and LXR knockout in HepG2 cells; xenograft nude mouse model; promoter analysis identifying LXR response element; CTU2 knockdown with proliferation and apoptosis readouts\",\n      \"journal\": \"Cell biology and toxicology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — LXR-CTU2 transcriptional regulation shown by agonist/KO plus promoter element, and lipogenesis/tumor role shown by KD in vitro and in vivo, but mechanistic detail on how CTU2 enhances lipogenic protein synthesis is not fully resolved in abstract\",\n      \"pmids\": [\"38630355\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"USF1 is identified as a transcription factor that regulates CTU2 expression; CTU2 overexpression in tumors is associated with DNA copy number amplification and DNA methylation alterations; CTU2 modifies tRNA-Lys-TTT at the wobble position.\",\n      \"method\": \"ChIP-seq data analysis, dual-luciferase reporter assay, EMSA for USF1 binding to CTU2 promoter; genomic copy number and methylation analysis from pan-cancer datasets; in vitro and in vivo oncogenic validation\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — USF1 regulation supported by dual-luciferase and EMSA (two orthogonal methods), single lab, no replication\",\n      \"pmids\": [\"40375999\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CTU2 (also known as NCS2/C16orf84) is an essential subunit of the conserved CTU1/CTU2 complex that catalyzes 2-thiolation of the wobble uridine (U34) in cytoplasmic tRNAs (tRNA-Lys, tRNA-Gln, tRNA-Glu); loss-of-function causes DREAM-PL syndrome in humans via global impairment of wobble uridine thiolation, while its expression is transcriptionally regulated by LXR (through a promoter LXR response element) and USF1, and it additionally promotes lipogenesis and tumor progression in hepatocellular carcinoma.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CTU2 is an essential subunit of the cytoplasmic CTU1/CTU2 thiolase complex that catalyzes 2-thiolation of the wobble uridine (U34) in the anticodon loop of tRNA-Lys, tRNA-Gln, and tRNA-Glu, a modification required for accurate decoding [#0]. In patient-derived cells, biallelic loss-of-function variants in CTU2 specifically abolish 2-thiolation across all wobble uridine-containing tRNAs, establishing the protein's catalytic indispensability and linking its loss to a human Mendelian disorder [#0]. The requirement of the CTU2 ortholog (Ncs2) for wobble uridine thiolation is conserved in yeast, where loss of 2-thiolation abrogates pathogenic virulence and complex stability and interaction depend on nucleotide binding [#1]. Beyond its tRNA-modifying role, CTU2 expression is transcriptionally activated by Liver X Receptor through a promoter LXR response element and by USF1, and CTU2 promotes lipogenesis and tumor progression in hepatocellular carcinoma, where its knockdown reduces tumor burden and synergizes with LXR ligands to induce apoptosis [#2, #3].\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Established that CTU2 is the catalytic determinant of wobble uridine 2-thiolation in human tRNAs and that its loss causes a defined biochemical and clinical phenotype.\",\n      \"evidence\": \"Functional characterization of patient-derived cells carrying five CTU2 alleles with direct biochemical thiolation readout\",\n      \"pmids\": [\"31301155\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of the CTU1/CTU2 catalytic mechanism not resolved\",\n        \"Downstream translational consequences of thiolation loss not directly mapped\",\n        \"Stoichiometry and assembly of the complex in human cells not defined\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed the thiolation function is evolutionarily conserved and physiologically consequential, with complex stability dependent on nucleotide binding and thiolation required for fungal virulence.\",\n      \"evidence\": \"Genetic and biochemical analysis of NCS2* point mutant, complex interaction/stability assays, and mouse and Candida albicans virulence models\",\n      \"pmids\": [\"37462076\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct extrapolation of yeast findings to human CTU2 not established\",\n        \"Nucleotide-binding site within the complex not structurally defined\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked CTU2 to lipid metabolism and cancer by identifying LXR-driven transcriptional control and a pro-lipogenic, pro-tumorigenic role in hepatocellular carcinoma.\",\n      \"evidence\": \"LXR agonist/knockout in HepG2 cells, promoter LXR response element analysis, CTU2 knockdown, and xenograft mouse model\",\n      \"pmids\": [\"38630355\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which CTU2 enhances lipogenic protein synthesis not resolved\",\n        \"Whether tumor effects depend on tRNA thiolation activity is untested\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended transcriptional regulation to USF1 and connected CTU2 overexpression to genomic and epigenetic alterations in cancer while confirming tRNA-Lys-TTT modification.\",\n      \"evidence\": \"ChIP-seq analysis, dual-luciferase reporter, EMSA for USF1 binding, pan-cancer copy number and methylation analysis, and oncogenic validation\",\n      \"pmids\": [\"40375999\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab USF1 regulation without independent replication\",\n        \"Causal link between copy number/methylation changes and CTU2 expression not established\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CTU2-dependent wobble uridine thiolation mechanistically couples to lipogenesis and tumor progression remains unresolved.\",\n      \"evidence\": \"No timeline discovery directly tests whether the oncogenic/lipogenic functions require catalytic thiolation activity\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of the human CTU1/CTU2 complex\",\n        \"Translational targets affected by thiolation loss not enumerated\",\n        \"Whether metabolic and disease roles are catalysis-dependent is unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\"CTU1/CTU2 thiolase complex\"],\n    \"partners\": [\"CTU1\", \"LXR\", \"USF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}