{"gene":"LTO1","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2013,"finding":"LTO1 (yeast YNL260c, ortholog of ORAOV1) is required for maturation of the 60S ribosomal subunit but not the 40S subunit, and for initiation of translation under aerobic conditions; loss of LTO1 function is lethal in oxygen but not under anaerobic conditions, linking its essential role to protection of ribosome biogenesis from reactive oxygen species.","method":"Conditional yeast mutants of YNL260c; ribosomal subunit maturation assays; translation initiation assays; complementation by human ORAOV1","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal functional assays (ribosome maturation, translation initiation, aerobic/anaerobic growth, complementation), replicated across yeast and human systems in a single focused study","pmids":["23318452"],"is_preprint":false},{"year":2013,"finding":"LTO1 forms a complex with Rli1/ABCE1 (an ABC-ATPase bearing N-terminal [4Fe-4S] clusters) and Yae1; Yae1 bridges the interaction between Lto1 and Rli1/ABCE1; interactions were demonstrated both in vivo and in vitro.","method":"In vivo co-immunoprecipitation and in vitro binding assays","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal in vivo and in vitro interaction assays in a single rigorous study with multiple orthogonal methods","pmids":["23318452"],"is_preprint":false},{"year":2015,"finding":"Yae1 and Lto1 function as target-specific adaptors for iron-sulfur (Fe-S) cluster insertion into Rli1/ABCE1: Lto1 uses its conserved C-terminal tryptophan to bind the CIA targeting complex, deca-GX3 motifs in both Yae1 and Lto1 mediate their heterocomplex formation, and Yae1 recruits apo-Rli1 to the CIA machinery. Depletion of Yae1 or Lto1 causes defective Fe-S maturation of Rli1 but not other tested CIA targets.","method":"Systematic protein interaction approaches (Co-IP, pulldown); depletion of Yae1/Lto1 followed by Fe-S maturation assays; C-terminal tryptophan mutagenesis; complementation with human YAE1D1 and ORAOV1","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — reconstitution of Fe-S insertion pathway, mutagenesis of key residue, multiple interaction methods, cross-species complementation, all in a single rigorous study","pmids":["26182403"],"is_preprint":false},{"year":2015,"finding":"Human ORAOV1 (LTO1) and YAE1D1 can functionally replace their yeast counterparts Lto1 and Yae1, demonstrating evolutionary conservation of their role in the CIA/Rli1 Fe-S assembly pathway.","method":"Complementation assay: expression of human genes in yeast deletion strains","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct genetic complementation in a rigorous study with multiple orthogonal methods","pmids":["26182403"],"is_preprint":false},{"year":2014,"finding":"ORAOV1 binds to pyrroline-5-carboxylate reductase (PYCR), leading to increased intracellular proline concentration and lower ROS levels; PYCR knockdown reverses the stress-resistance phenotype of ORAOV1-overexpressing esophageal cancer cells.","method":"Peptide mass fingerprinting (co-purification/MS); PYCR knockdown rescue assay; intracellular proline and ROS measurements","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — MS-based interaction identification plus functional rescue, single lab, but two orthogonal approaches","pmids":["24930674"],"is_preprint":false},{"year":2008,"finding":"siRNA-mediated knockdown of ORAOV1 in oral squamous cell carcinoma cells causes S-phase cell cycle arrest with downregulation of cyclin A, cyclin B1, and CDC2, and activates caspase-3-dependent apoptosis; in vivo, ORAOV1 knockdown inhibits tumor growth and suppresses VEGF-dependent tumor angiogenesis.","method":"siRNA knockdown; cell cycle analysis; apoptosis assays; xenograft tumor model; VEGF measurement","journal":"International journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — loss-of-function with defined cellular and molecular phenotypes, both in vitro and in vivo, single lab","pmids":["18688849"],"is_preprint":false},{"year":2010,"finding":"Knockdown of ORAOV1 in HeLa cervical cancer cells causes S-phase arrest with downregulation of Cyclin A, Cyclin B1, CDC2, and Cyclin D1, and activates both extrinsic (Caspase-8) and intrinsic (Caspase-9, cytochrome c) apoptotic pathways, with altered P53 and Bcl-2 expression.","method":"siRNA knockdown; cell cycle analysis; apoptosis pathway protein analysis by Western blot","journal":"Molecular cancer","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — siRNA KD with multiple downstream readouts, independent replication of OSCC findings in a second cancer cell type, single lab","pmids":["20105337"],"is_preprint":false},{"year":2017,"finding":"IBDV VP2 protein interacts with ORAOV1 and causes its degradation; ORAOV1 reduction mediates VP2-induced apoptosis, whereas ORAOV1 overexpression inhibits VP2/IBDV-induced apoptosis and restricts viral release, identifying ORAOV1 as an antiapoptotic molecule.","method":"Co-immunoprecipitation (VP2–ORAOV1 interaction); overexpression and knockdown of ORAOV1; apoptosis and viral release assays","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP plus bidirectional gain/loss-of-function, single lab, avian cell system","pmids":["28769911"],"is_preprint":false},{"year":2024,"finding":"ORAOV1 functions as an oncogenic driver in the 11q13 amplicon in squamous cell carcinoma, acting likely via modulation of reactive oxygen species, as identified by computational, in vitro, ex vivo, and in vivo models using primary human keratinocyte Cas9-RNP genome editing.","method":"CRISPR-Cas9 KO in primary human keratinocytes; in vitro, ex vivo, in vivo models; ROS measurement","journal":"Molecular cancer research : MCR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR KO with functional phenotypes in multiple model systems, single lab, mechanism inferred rather than fully reconstituted","pmids":["37930255"],"is_preprint":false},{"year":2025,"finding":"The LTO1/YAE1 complex regulates nonsense-mediated mRNA decay (NMD); deficiency in LTO1, YAE1, or their downstream target ABCE1 impairs NMD, leading to overexpression of MHC-I regulators NLRC5, IRF1, and NF-κB, enhanced T cell activation, and tumor cell killing. Iron chelators, by inhibiting NMD via the LTO1/YAE1/ABCE1 axis, enhance MHC-I expression and improve anti-tumor immune responses.","method":"CRISPR-Cas9 KO and overexpression; fluorescent NMD reporter assays; FACS; RT-qPCR; mRNA decay assays; polysome profiling; TCR-T cell coculture; in vivo mouse tumor model","journal":"Journal for immunotherapy of cancer","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal mechanistic methods (reporter assay, mRNA decay, polysome profiling, CRISPR KO, in vivo model) establishing NMD as downstream mechanism in a single rigorous study","pmids":["40987494"],"is_preprint":false}],"current_model":"LTO1/ORAOV1 forms a target-specific adaptor complex with YAE1 that recruits apo-ABCE1/Rli1 to the cytosolic iron-sulfur cluster assembly (CIA) machinery for Fe-S cluster insertion, which is required for 60S ribosomal subunit biogenesis and translation initiation under aerobic conditions; the LTO1/YAE1/ABCE1 axis additionally acts as a component of nonsense-mediated mRNA decay, suppressing MHC-I antigen presentation in tumor cells, while ORAOV1 overexpression in cancer also modulates reactive oxygen species (likely via PYCR-mediated proline metabolism) and promotes cell cycle progression and angiogenesis."},"narrative":{"mechanistic_narrative":"LTO1 (ORAOV1) is a target-specific adaptor for iron-sulfur (Fe-S) cluster delivery that couples the cytosolic Fe-S assembly (CIA) machinery to the ribosome-recycling/translation factor ABCE1/Rli1, thereby supporting 60S ribosomal subunit maturation and translation initiation under aerobic conditions [PMID:23318452, PMID:26182403]. It forms a heterodimer with YAE1 in which deca-GX3 motifs in both proteins mediate their interaction, LTO1 uses a conserved C-terminal tryptophan to engage the CIA targeting complex, and YAE1 bridges recruitment of apo-ABCE1/Rli1 for Fe-S insertion; depletion of either adaptor selectively impairs Fe-S maturation of Rli1 but not other CIA targets [PMID:23318452, PMID:26182403]. This adaptor function is evolutionarily conserved, as human ORAOV1 and YAE1D1 functionally replace their yeast counterparts [PMID:26182403]. Through its control of ABCE1, the LTO1/YAE1 axis is required for nonsense-mediated mRNA decay (NMD), and loss of this axis impairs NMD, derepressing MHC-I regulators NLRC5, IRF1, and NF-κB to enhance T cell-mediated tumor killing [PMID:40987494]. In cancer cells ORAOV1 additionally binds pyrroline-5-carboxylate reductase (PYCR) to raise intracellular proline and lower reactive oxygen species, and acts as an 11q13-amplicon oncogenic driver promoting cell cycle progression, survival, and tumor angiogenesis [PMID:24930674, PMID:18688849, PMID:37930255].","teleology":[{"year":2013,"claim":"Established the core cellular function of LTO1 by showing it is specifically required for 60S subunit maturation and aerobic translation initiation, linking it to ribosome biogenesis under oxidative conditions.","evidence":"Conditional yeast YNL260c mutants with ribosomal maturation and translation assays, plus human ORAOV1 complementation","pmids":["23318452"],"confidence":"High","gaps":["Did not yet define the molecular mechanism connecting LTO1 to 60S maturation","Oxygen-dependence mechanism inferred rather than directly demonstrated"]},{"year":2013,"claim":"Identified the physical partners of LTO1, showing it assembles with YAE1 and the Fe-S-bearing ATPase Rli1/ABCE1, with YAE1 bridging the LTO1-Rli1 interaction.","evidence":"In vivo co-immunoprecipitation and in vitro binding assays","pmids":["23318452"],"confidence":"High","gaps":["Did not define which residues mediate complex assembly","Functional consequence of the interaction for Fe-S loading not yet shown"]},{"year":2015,"claim":"Resolved the mechanism by defining LTO1/YAE1 as a target-specific CIA adaptor that delivers Fe-S clusters selectively to apo-Rli1/ABCE1, via a C-terminal tryptophan and deca-GX3 motifs.","evidence":"Systematic interaction mapping, Yae1/Lto1 depletion with Fe-S maturation assays, tryptophan mutagenesis, and human gene complementation","pmids":["26182403"],"confidence":"High","gaps":["Structural basis of CIA-targeting-complex recognition not resolved","Whether additional targets exist beyond Rli1 not exhaustively tested"]},{"year":2015,"claim":"Demonstrated evolutionary conservation by showing human ORAOV1 and YAE1D1 substitute for yeast Lto1/Yae1 in the Fe-S delivery pathway.","evidence":"Cross-species genetic complementation in yeast deletion strains","pmids":["26182403"],"confidence":"High","gaps":["Conservation of the human pathway not validated directly in human cells in this work"]},{"year":2025,"claim":"Connected the LTO1/YAE1/ABCE1 axis to a downstream physiological output by showing it is required for NMD, and that its loss derepresses MHC-I and enhances anti-tumor immunity.","evidence":"CRISPR KO/overexpression, NMD reporter and mRNA decay assays, polysome profiling, TCR-T coculture, and in vivo tumor models","pmids":["40987494"],"confidence":"High","gaps":["Direct biochemical step in NMD requiring ABCE1 Fe-S not isolated","How iron chelators inhibit the axis mechanistically not fully resolved"]},{"year":2014,"claim":"Linked ORAOV1 to redox homeostasis in cancer by showing it binds PYCR to elevate proline and reduce ROS, conferring stress resistance.","evidence":"MS-based co-purification, PYCR knockdown rescue, and proline/ROS measurements in esophageal cancer cells","pmids":["24930674"],"confidence":"Medium","gaps":["Single lab; PYCR interaction not reciprocally validated","Relationship between this metabolic role and the Fe-S adaptor role unclear"]},{"year":2008,"claim":"Defined ORAOV1 as a pro-proliferative, anti-apoptotic, and pro-angiogenic factor in oral squamous cell carcinoma.","evidence":"siRNA knockdown with cell cycle, apoptosis, xenograft, and VEGF assays","pmids":["18688849"],"confidence":"Medium","gaps":["Molecular link between adaptor function and cell cycle phenotype not established","Effects could be indirect consequences of impaired translation"]},{"year":2010,"claim":"Replicated and extended the cancer phenotype in a second cell type, mapping ORAOV1 loss to S-phase arrest and activation of both apoptotic pathways.","evidence":"siRNA knockdown with cell cycle analysis and apoptosis pathway Western blots in HeLa cells","pmids":["20105337"],"confidence":"Medium","gaps":["Mechanism connecting ORAOV1 to cyclin/caspase regulation not defined","Single lab"]},{"year":2017,"claim":"Identified ORAOV1 as an anti-apoptotic host factor targeted for degradation by IBDV VP2 during viral infection.","evidence":"Co-IP and bidirectional gain/loss-of-function with apoptosis and viral release assays in avian cells","pmids":["28769911"],"confidence":"Medium","gaps":["Mechanism of VP2-induced degradation not defined","Relevance to mammalian/human biology unclear"]},{"year":2024,"claim":"Validated ORAOV1 as a bona fide oncogenic driver within the 11q13 amplicon in squamous cell carcinoma, acting via ROS modulation.","evidence":"CRISPR-Cas9 KO in primary human keratinocytes with in vitro, ex vivo, and in vivo models plus ROS measurement","pmids":["37930255"],"confidence":"Medium","gaps":["ROS mechanism inferred rather than reconstituted","Whether the oncogenic effect operates through the Fe-S adaptor role unresolved"]},{"year":null,"claim":"How LTO1's conserved Fe-S adaptor function mechanistically integrates with its observed redox, cell cycle, and oncogenic roles in cancer remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the human ORAOV1/YAE1D1/ABCE1 complex","Unclear whether cancer phenotypes derive from impaired ABCE1 Fe-S loading or separate activities"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,2]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[9]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0]}],"complexes":["LTO1-YAE1 adaptor complex","CIA targeting complex (associated)"],"partners":["YAE1","ABCE1","PYCR"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8WV07","full_name":"Protein LTO1 homolog","aliases":["Oral cancer-overexpressed protein 1","Tumor-amplified and overexpressed sequence 1"],"length_aa":137,"mass_kda":15.4,"function":"The complex LTO1:YAE1 functions as a target specific adapter that probably recruits apo-ABCE1 to the cytosolic iron-sulfur protein assembly (CIA) complex machinery (PubMed:26182403). May be required for biogenesis of the large ribosomal subunit and initiation of translation (PubMed:23318452). May play a role in the regulation of proline metabolism and ROS production (PubMed:24930674)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8WV07/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/LTO1","classification":"Common Essential","n_dependent_lines":1203,"n_total_lines":1208,"dependency_fraction":0.9958609271523179},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ABCE1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/LTO1","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/LTO1"},"hgnc":{"alias_symbol":["TAOS1","CIAB1"],"prev_symbol":["ORAOV1"]},"alphafold":{"accession":"Q8WV07","domains":[{"cath_id":"-","chopping":"8-119","consensus_level":"medium","plddt":89.9959,"start":8,"end":119}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8WV07","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8WV07-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8WV07-F1-predicted_aligned_error_v6.png","plddt_mean":84.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LTO1","jax_strain_url":"https://www.jax.org/strain/search?query=LTO1"},"sequence":{"accession":"Q8WV07","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8WV07.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8WV07/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8WV07"}},"corpus_meta":[{"pmid":"12172009","id":"PMC_12172009","title":"High-resolution mapping of the 11q13 amplicon and identification of a gene, TAOS1, that is amplified and overexpressed in oral cancer cells.","date":"2002","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12172009","citation_count":171,"is_preprint":false},{"pmid":"17906623","id":"PMC_17906623","title":"Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs.","date":"2007","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/17906623","citation_count":156,"is_preprint":false},{"pmid":"12792807","id":"PMC_12792807","title":"Evolutionary conservation of CCND1-ORAOV1-FGF19-FGF4 locus from zebrafish to human.","date":"2003","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/12792807","citation_count":116,"is_preprint":false},{"pmid":"26182403","id":"PMC_26182403","title":"The deca-GX3 proteins Yae1-Lto1 function as adaptors recruiting the ABC protein Rli1 for iron-sulfur cluster insertion.","date":"2015","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/26182403","citation_count":53,"is_preprint":false},{"pmid":"24930674","id":"PMC_24930674","title":"Frequent amplification of ORAOV1 gene in esophageal squamous cell cancer promotes an aggressive phenotype via proline metabolism and ROS production.","date":"2014","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/24930674","citation_count":52,"is_preprint":false},{"pmid":"18688849","id":"PMC_18688849","title":"Oral cancer overexpressed 1 (ORAOV1): a regulator for the cell growth and tumor angiogenesis in oral squamous cell carcinoma.","date":"2008","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/18688849","citation_count":48,"is_preprint":false},{"pmid":"17005439","id":"PMC_17005439","title":"Amplifications of TAOS1 and EMS1 genes in oral carcinogenesis: association with clinicopathological features.","date":"2006","source":"Oral oncology","url":"https://pubmed.ncbi.nlm.nih.gov/17005439","citation_count":39,"is_preprint":false},{"pmid":"20105337","id":"PMC_20105337","title":"Oral cancer overexpressed 1 (ORAOV1) regulates cell cycle and apoptosis in cervical cancer HeLa cells.","date":"2010","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/20105337","citation_count":35,"is_preprint":false},{"pmid":"23318452","id":"PMC_23318452","title":"The function of ORAOV1/LTO1, a gene that is overexpressed frequently in cancer: essential roles in the function and biogenesis of the ribosome.","date":"2013","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/23318452","citation_count":34,"is_preprint":false},{"pmid":"28769911","id":"PMC_28769911","title":"VP2 of Infectious Bursal Disease Virus Induces Apoptosis via Triggering Oral Cancer Overexpressed 1 (ORAOV1) Protein Degradation.","date":"2017","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/28769911","citation_count":25,"is_preprint":false},{"pmid":"33655785","id":"PMC_33655785","title":"ORAOV1-B Promotes OSCC Metastasis via the NF-κB-TNFα Loop.","date":"2021","source":"Journal of dental research","url":"https://pubmed.ncbi.nlm.nih.gov/33655785","citation_count":23,"is_preprint":false},{"pmid":"16827140","id":"PMC_16827140","title":"TAOS1, a novel marker for advanced esophageal squamous cell carcinoma.","date":"2006","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/16827140","citation_count":23,"is_preprint":false},{"pmid":"19493886","id":"PMC_19493886","title":"ORAOV1-A correlates with poor differentiation in oral cancer.","date":"2009","source":"Journal of dental research","url":"https://pubmed.ncbi.nlm.nih.gov/19493886","citation_count":13,"is_preprint":false},{"pmid":"21993861","id":"PMC_21993861","title":"ORAOV1 is a probable target within the 11q13.3 amplicon in lymph node metastases from gastric adenocarcinoma.","date":"2011","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/21993861","citation_count":12,"is_preprint":false},{"pmid":"21623924","id":"PMC_21623924","title":"ORAOV1 is amplified in oral squamous cell carcinoma.","date":"2011","source":"Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology","url":"https://pubmed.ncbi.nlm.nih.gov/21623924","citation_count":10,"is_preprint":false},{"pmid":"25412899","id":"PMC_25412899","title":"Identification of potential targets for thylakoid oxidoreductase AtVKOR/LTO1 in chloroplasts.","date":"2014","source":"Protein and peptide letters","url":"https://pubmed.ncbi.nlm.nih.gov/25412899","citation_count":7,"is_preprint":false},{"pmid":"37930255","id":"PMC_37930255","title":"ORAOV1, CCND1, and MIR548K Are the Driver Oncogenes of the 11q13 Amplicon in Squamous Cell 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MHC-I expression via nonsense-mediated RNA decay in tumor cells.","date":"2025","source":"Journal for immunotherapy of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40987494","citation_count":0,"is_preprint":false},{"pmid":"41321947","id":"PMC_41321947","title":"Overexpression of ORAOV1 and its association with immunotherapy resistance in hepatocellular carcinoma.","date":"2025","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/41321947","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13130,"output_tokens":2657,"usd":0.039622,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9850,"output_tokens":3271,"usd":0.065513,"stage2_stop_reason":"end_turn"},"total_usd":0.105135,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"LTO1 (yeast YNL260c, ortholog of ORAOV1) is required for maturation of the 60S ribosomal subunit but not the 40S subunit, and for initiation of translation under aerobic conditions; loss of LTO1 function is lethal in oxygen but not under anaerobic conditions, linking its essential role to protection of ribosome biogenesis from reactive oxygen species.\",\n      \"method\": \"Conditional yeast mutants of YNL260c; ribosomal subunit maturation assays; translation initiation assays; complementation by human ORAOV1\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal functional assays (ribosome maturation, translation initiation, aerobic/anaerobic growth, complementation), replicated across yeast and human systems in a single focused study\",\n      \"pmids\": [\"23318452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"LTO1 forms a complex with Rli1/ABCE1 (an ABC-ATPase bearing N-terminal [4Fe-4S] clusters) and Yae1; Yae1 bridges the interaction between Lto1 and Rli1/ABCE1; interactions were demonstrated both in vivo and in vitro.\",\n      \"method\": \"In vivo co-immunoprecipitation and in vitro binding assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal in vivo and in vitro interaction assays in a single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"23318452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Yae1 and Lto1 function as target-specific adaptors for iron-sulfur (Fe-S) cluster insertion into Rli1/ABCE1: Lto1 uses its conserved C-terminal tryptophan to bind the CIA targeting complex, deca-GX3 motifs in both Yae1 and Lto1 mediate their heterocomplex formation, and Yae1 recruits apo-Rli1 to the CIA machinery. Depletion of Yae1 or Lto1 causes defective Fe-S maturation of Rli1 but not other tested CIA targets.\",\n      \"method\": \"Systematic protein interaction approaches (Co-IP, pulldown); depletion of Yae1/Lto1 followed by Fe-S maturation assays; C-terminal tryptophan mutagenesis; complementation with human YAE1D1 and ORAOV1\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — reconstitution of Fe-S insertion pathway, mutagenesis of key residue, multiple interaction methods, cross-species complementation, all in a single rigorous study\",\n      \"pmids\": [\"26182403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Human ORAOV1 (LTO1) and YAE1D1 can functionally replace their yeast counterparts Lto1 and Yae1, demonstrating evolutionary conservation of their role in the CIA/Rli1 Fe-S assembly pathway.\",\n      \"method\": \"Complementation assay: expression of human genes in yeast deletion strains\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct genetic complementation in a rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"26182403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ORAOV1 binds to pyrroline-5-carboxylate reductase (PYCR), leading to increased intracellular proline concentration and lower ROS levels; PYCR knockdown reverses the stress-resistance phenotype of ORAOV1-overexpressing esophageal cancer cells.\",\n      \"method\": \"Peptide mass fingerprinting (co-purification/MS); PYCR knockdown rescue assay; intracellular proline and ROS measurements\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — MS-based interaction identification plus functional rescue, single lab, but two orthogonal approaches\",\n      \"pmids\": [\"24930674\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"siRNA-mediated knockdown of ORAOV1 in oral squamous cell carcinoma cells causes S-phase cell cycle arrest with downregulation of cyclin A, cyclin B1, and CDC2, and activates caspase-3-dependent apoptosis; in vivo, ORAOV1 knockdown inhibits tumor growth and suppresses VEGF-dependent tumor angiogenesis.\",\n      \"method\": \"siRNA knockdown; cell cycle analysis; apoptosis assays; xenograft tumor model; VEGF measurement\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — loss-of-function with defined cellular and molecular phenotypes, both in vitro and in vivo, single lab\",\n      \"pmids\": [\"18688849\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Knockdown of ORAOV1 in HeLa cervical cancer cells causes S-phase arrest with downregulation of Cyclin A, Cyclin B1, CDC2, and Cyclin D1, and activates both extrinsic (Caspase-8) and intrinsic (Caspase-9, cytochrome c) apoptotic pathways, with altered P53 and Bcl-2 expression.\",\n      \"method\": \"siRNA knockdown; cell cycle analysis; apoptosis pathway protein analysis by Western blot\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — siRNA KD with multiple downstream readouts, independent replication of OSCC findings in a second cancer cell type, single lab\",\n      \"pmids\": [\"20105337\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"IBDV VP2 protein interacts with ORAOV1 and causes its degradation; ORAOV1 reduction mediates VP2-induced apoptosis, whereas ORAOV1 overexpression inhibits VP2/IBDV-induced apoptosis and restricts viral release, identifying ORAOV1 as an antiapoptotic molecule.\",\n      \"method\": \"Co-immunoprecipitation (VP2–ORAOV1 interaction); overexpression and knockdown of ORAOV1; apoptosis and viral release assays\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP plus bidirectional gain/loss-of-function, single lab, avian cell system\",\n      \"pmids\": [\"28769911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ORAOV1 functions as an oncogenic driver in the 11q13 amplicon in squamous cell carcinoma, acting likely via modulation of reactive oxygen species, as identified by computational, in vitro, ex vivo, and in vivo models using primary human keratinocyte Cas9-RNP genome editing.\",\n      \"method\": \"CRISPR-Cas9 KO in primary human keratinocytes; in vitro, ex vivo, in vivo models; ROS measurement\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR KO with functional phenotypes in multiple model systems, single lab, mechanism inferred rather than fully reconstituted\",\n      \"pmids\": [\"37930255\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The LTO1/YAE1 complex regulates nonsense-mediated mRNA decay (NMD); deficiency in LTO1, YAE1, or their downstream target ABCE1 impairs NMD, leading to overexpression of MHC-I regulators NLRC5, IRF1, and NF-κB, enhanced T cell activation, and tumor cell killing. Iron chelators, by inhibiting NMD via the LTO1/YAE1/ABCE1 axis, enhance MHC-I expression and improve anti-tumor immune responses.\",\n      \"method\": \"CRISPR-Cas9 KO and overexpression; fluorescent NMD reporter assays; FACS; RT-qPCR; mRNA decay assays; polysome profiling; TCR-T cell coculture; in vivo mouse tumor model\",\n      \"journal\": \"Journal for immunotherapy of cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal mechanistic methods (reporter assay, mRNA decay, polysome profiling, CRISPR KO, in vivo model) establishing NMD as downstream mechanism in a single rigorous study\",\n      \"pmids\": [\"40987494\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LTO1/ORAOV1 forms a target-specific adaptor complex with YAE1 that recruits apo-ABCE1/Rli1 to the cytosolic iron-sulfur cluster assembly (CIA) machinery for Fe-S cluster insertion, which is required for 60S ribosomal subunit biogenesis and translation initiation under aerobic conditions; the LTO1/YAE1/ABCE1 axis additionally acts as a component of nonsense-mediated mRNA decay, suppressing MHC-I antigen presentation in tumor cells, while ORAOV1 overexpression in cancer also modulates reactive oxygen species (likely via PYCR-mediated proline metabolism) and promotes cell cycle progression and angiogenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LTO1 (ORAOV1) is a target-specific adaptor for iron-sulfur (Fe-S) cluster delivery that couples the cytosolic Fe-S assembly (CIA) machinery to the ribosome-recycling/translation factor ABCE1/Rli1, thereby supporting 60S ribosomal subunit maturation and translation initiation under aerobic conditions [#0, #2]. It forms a heterodimer with YAE1 in which deca-GX3 motifs in both proteins mediate their interaction, LTO1 uses a conserved C-terminal tryptophan to engage the CIA targeting complex, and YAE1 bridges recruitment of apo-ABCE1/Rli1 for Fe-S insertion; depletion of either adaptor selectively impairs Fe-S maturation of Rli1 but not other CIA targets [#1, #2]. This adaptor function is evolutionarily conserved, as human ORAOV1 and YAE1D1 functionally replace their yeast counterparts [#3]. Through its control of ABCE1, the LTO1/YAE1 axis is required for nonsense-mediated mRNA decay (NMD), and loss of this axis impairs NMD, derepressing MHC-I regulators NLRC5, IRF1, and NF-\\u03baB to enhance T cell-mediated tumor killing [#9]. In cancer cells ORAOV1 additionally binds pyrroline-5-carboxylate reductase (PYCR) to raise intracellular proline and lower reactive oxygen species, and acts as an 11q13-amplicon oncogenic driver promoting cell cycle progression, survival, and tumor angiogenesis [#4, #5, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established the core cellular function of LTO1 by showing it is specifically required for 60S subunit maturation and aerobic translation initiation, linking it to ribosome biogenesis under oxidative conditions.\",\n      \"evidence\": \"Conditional yeast YNL260c mutants with ribosomal maturation and translation assays, plus human ORAOV1 complementation\",\n      \"pmids\": [\"23318452\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not yet define the molecular mechanism connecting LTO1 to 60S maturation\", \"Oxygen-dependence mechanism inferred rather than directly demonstrated\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identified the physical partners of LTO1, showing it assembles with YAE1 and the Fe-S-bearing ATPase Rli1/ABCE1, with YAE1 bridging the LTO1-Rli1 interaction.\",\n      \"evidence\": \"In vivo co-immunoprecipitation and in vitro binding assays\",\n      \"pmids\": [\"23318452\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which residues mediate complex assembly\", \"Functional consequence of the interaction for Fe-S loading not yet shown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Resolved the mechanism by defining LTO1/YAE1 as a target-specific CIA adaptor that delivers Fe-S clusters selectively to apo-Rli1/ABCE1, via a C-terminal tryptophan and deca-GX3 motifs.\",\n      \"evidence\": \"Systematic interaction mapping, Yae1/Lto1 depletion with Fe-S maturation assays, tryptophan mutagenesis, and human gene complementation\",\n      \"pmids\": [\"26182403\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of CIA-targeting-complex recognition not resolved\", \"Whether additional targets exist beyond Rli1 not exhaustively tested\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated evolutionary conservation by showing human ORAOV1 and YAE1D1 substitute for yeast Lto1/Yae1 in the Fe-S delivery pathway.\",\n      \"evidence\": \"Cross-species genetic complementation in yeast deletion strains\",\n      \"pmids\": [\"26182403\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conservation of the human pathway not validated directly in human cells in this work\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected the LTO1/YAE1/ABCE1 axis to a downstream physiological output by showing it is required for NMD, and that its loss derepresses MHC-I and enhances anti-tumor immunity.\",\n      \"evidence\": \"CRISPR KO/overexpression, NMD reporter and mRNA decay assays, polysome profiling, TCR-T coculture, and in vivo tumor models\",\n      \"pmids\": [\"40987494\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct biochemical step in NMD requiring ABCE1 Fe-S not isolated\", \"How iron chelators inhibit the axis mechanistically not fully resolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked ORAOV1 to redox homeostasis in cancer by showing it binds PYCR to elevate proline and reduce ROS, conferring stress resistance.\",\n      \"evidence\": \"MS-based co-purification, PYCR knockdown rescue, and proline/ROS measurements in esophageal cancer cells\",\n      \"pmids\": [\"24930674\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; PYCR interaction not reciprocally validated\", \"Relationship between this metabolic role and the Fe-S adaptor role unclear\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defined ORAOV1 as a pro-proliferative, anti-apoptotic, and pro-angiogenic factor in oral squamous cell carcinoma.\",\n      \"evidence\": \"siRNA knockdown with cell cycle, apoptosis, xenograft, and VEGF assays\",\n      \"pmids\": [\"18688849\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between adaptor function and cell cycle phenotype not established\", \"Effects could be indirect consequences of impaired translation\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Replicated and extended the cancer phenotype in a second cell type, mapping ORAOV1 loss to S-phase arrest and activation of both apoptotic pathways.\",\n      \"evidence\": \"siRNA knockdown with cell cycle analysis and apoptosis pathway Western blots in HeLa cells\",\n      \"pmids\": [\"20105337\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting ORAOV1 to cyclin/caspase regulation not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identified ORAOV1 as an anti-apoptotic host factor targeted for degradation by IBDV VP2 during viral infection.\",\n      \"evidence\": \"Co-IP and bidirectional gain/loss-of-function with apoptosis and viral release assays in avian cells\",\n      \"pmids\": [\"28769911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of VP2-induced degradation not defined\", \"Relevance to mammalian/human biology unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Validated ORAOV1 as a bona fide oncogenic driver within the 11q13 amplicon in squamous cell carcinoma, acting via ROS modulation.\",\n      \"evidence\": \"CRISPR-Cas9 KO in primary human keratinocytes with in vitro, ex vivo, and in vivo models plus ROS measurement\",\n      \"pmids\": [\"37930255\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ROS mechanism inferred rather than reconstituted\", \"Whether the oncogenic effect operates through the Fe-S adaptor role unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How LTO1's conserved Fe-S adaptor function mechanistically integrates with its observed redox, cell cycle, and oncogenic roles in cancer remains unresolved.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the human ORAOV1/YAE1D1/ABCE1 complex\", \"Unclear whether cancer phenotypes derive from impaired ABCE1 Fe-S loading or separate activities\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"LTO1-YAE1 adaptor complex\", \"CIA targeting complex (associated)\"],\n    \"partners\": [\"YAE1\", \"ABCE1\", \"PYCR\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}