{"gene":"TTC7B","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2021,"finding":"TTC7B is a component of the plasma membrane-localized phosphatidylinositol 4-kinase (PI4KA) complex, which also contains EFR3B, PI4KA, and FAM126A. Palmitoylated CNAβ1 (calcineurin isoform) was shown to interact with this complex, and calcineurin was identified to dephosphorylate FAM126A, promoting PI4KA complex activity and PI4P production during Gq-coupled GPCR signaling.","method":"Hydrogen-deuterium exchange mass spectrometry, Co-immunoprecipitation, calcineurin substrate identification, phosphatidylinositol 4-phosphate production assay, palmitoylation/depalmitoylation experiments","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — HDX-MS plus reciprocal interaction mapping, substrate phosphorylation assay, and functional PI4P production readout in a single study","pmids":["34663815"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structure of EFR3A C-terminus bound to the PI4KA-TTC7B-FAM126A complex revealed that the EFR3A C-terminus undergoes a disorder-to-order transition upon binding, making direct contacts with both TTC7B and FAM126A. Complex-disrupting mutations in TTC7B, FAM126A, and EFR3 decrease PI4KA recruitment to the plasma membrane.","method":"Cryo-electron microscopy (cryo-EM), hydrogen-deuterium exchange mass spectrometry (HDX-MS), mutational analysis, plasma membrane recruitment assay","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution cryo-EM structure with HDX-MS validation and mutational functional analysis; replicated in preprint (PMID:38746453)","pmids":["39705356","38746453"],"is_preprint":false},{"year":2025,"finding":"A TTC7B-selective nanobody was developed that sterically blocks EFR3 binding to TTC7B-containing PI4KA complexes. Cryo-EM and HDX-MS showed the nanobody forms an extended interface with both PI4KA and TTC7B. The nanobody caused decreased PI4KA membrane recruitment on lipid bilayers and in cells, with reduced plasma membrane PI4P production. EFR3A-TTC7B-FAM126A binds with ~10-fold higher affinity than most other EFR3-TTC7-FAM126 combinations, and EFR3B phosphorylation markedly decreases binding to TTC7-FAM126.","method":"Yeast display nanobody selection, cryo-EM, HDX-MS, lipid bilayer reconstitution assay, cellular PI4P production assay, binding affinity measurements","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure, HDX-MS, reconstituted lipid bilayer assay, and cellular readouts in single study; preprint version also available (PMID:41473329)","pmids":["41197736","41473329"],"is_preprint":false},{"year":2012,"finding":"TTC7B (tetratricopeptide repeat protein 7B) was identified as a binding partner of Chikungunya virus nonstructural protein nsP2 by yeast two-hybrid assay, and gene silencing experiments showed TTC7B plays a significant role in nsP2-induced cellular shutoff activity.","method":"High-throughput yeast two-hybrid (HT-Y2H), protein complementation assay (PCA), gene silencing with luciferase reporter assay","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — Y2H interaction validated by PCA and siRNA knockdown in a single study, but functional mechanism downstream of TTC7B-nsP2 interaction not fully resolved","pmids":["22258240"],"is_preprint":false},{"year":2025,"finding":"TTC7B activates AKT1 signaling (via its role as a PI4KA-binding protein), which upregulates RXRA expression. RXRA acts as a transcription factor for the FTO gene, increasing FTO expression and decreasing total RNA m6A modification. TTC7B inhibited colon cancer cell proliferation through this PI4KA-AKT1-RXRA-FTO axis; ablation of FTO demethylase activity abolished TTC7B's antiproliferative effect in vitro and in vivo.","method":"Biological experiments in colon cancer cell lines and xenografts, transcription factor binding assay (RXRA recruitment to FTO promoter), m6A quantification, FTO activity ablation, in vivo tumor models","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — multiple functional assays and in vivo data from a single lab, but mechanistic links between PI4KA binding and AKT1 activation by TTC7B not directly biochemically resolved","pmids":["39897037"],"is_preprint":false},{"year":2026,"finding":"GIPC1 reduces ubiquitination of TTC7B by downregulating the E3 ubiquitin ligase TRIM21, thereby stabilizing TTC7B protein expression. Stabilized TTC7B in turn inhibits downstream mTOR/NF-κB signaling, suppressing colorectal cancer cell proliferation, migration, invasion, and chemoresistance.","method":"Ubiquitination assay, E3 ligase knockdown, in vitro functional assays (proliferation, migration, invasion), in vivo tumor models, GIPC1-loaded lipid nanoparticles combined with 5-FU","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — ubiquitination assay identifies TRIM21 as TTC7B E3 ligase with in vivo validation, but all from a single lab","pmids":["41522336"],"is_preprint":false},{"year":2025,"finding":"TTC7B promotes head and neck cancer (HNC) cell migration and invasion through activation of AKT, which upregulates JKAMP. Pharmacological AKT inhibition abolished TTC7B-induced AKT phosphorylation and JKAMP expression, suppressing migration and invasion. IGF-1-mediated AKT activation rescued TTC7B-knockdown phenotypes, and JKAMP silencing in TTC7B-overexpressing cells reduced migration and invasion.","method":"In vitro migration/invasion assays, TTC7B knockdown and overexpression, AKT pharmacological inhibition, IGF-1 stimulation rescue experiments, JKAMP silencing","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — multiple epistasis-style rescue experiments in cell lines from a single lab; no direct biochemical reconstitution of TTC7B-AKT interaction","pmids":["41392613"],"is_preprint":false}],"current_model":"TTC7B is a scaffold protein that forms a stable heterotrimeric complex with PI4KA and FAM126, recruited to the plasma membrane by EFR3A/B; structural and mutational studies show TTC7B directly contacts EFR3 to position PI4KA for phosphatidylinositol 4-phosphate production, while additional studies indicate TTC7B modulates AKT/mTOR/NF-κB signaling and is itself regulated by TRIM21-mediated ubiquitination, and its stability and activity are further controlled by calcineurin-mediated dephosphorylation of the complex."},"narrative":{"mechanistic_narrative":"TTC7B is a scaffold subunit of the plasma membrane phosphatidylinositol 4-kinase (PI4KA) complex, where it bridges the catalytic kinase PI4KA, FAM126A, and the membrane anchor EFR3 to drive phosphatidylinositol 4-phosphate (PI4P) production [PMID:34663815, PMID:39705356, PMID:38746453]. Cryo-EM and HDX-MS analyses show that the EFR3A C-terminus undergoes a disorder-to-order transition upon binding and makes direct contacts with both TTC7B and FAM126A, and that complex-disrupting mutations in TTC7B reduce PI4KA recruitment to the plasma membrane [PMID:39705356, PMID:38746453]; the EFR3A-TTC7B-FAM126A combination binds with ~10-fold higher affinity than most other EFR3-TTC7-FAM126 pairings, and sterically blocking the EFR3-TTC7B interface with a selective nanobody decreases PI4KA membrane recruitment and PI4P production [PMID:41197736, PMID:41473329]. Assembly and activity of the complex are dynamically regulated: calcineurin dephosphorylates FAM126A to promote PI4KA activity and PI4P production during Gq-coupled GPCR signaling, while EFR3B phosphorylation markedly weakens binding to TTC7-FAM126 [PMID:34663815, PMID:41197736, PMID:41473329]. Through its PI4KA-linked role, TTC7B modulates AKT signaling with context-dependent outcomes in cancer: it activates a PI4KA-AKT1-RXRA-FTO axis that lowers RNA m6A and suppresses colon cancer proliferation [PMID:39897037], yet activates AKT-dependent JKAMP induction that promotes head and neck cancer migration and invasion [PMID:41392613]. TTC7B protein levels are controlled by TRIM21-mediated ubiquitination, which is antagonized by GIPC1, and stabilized TTC7B suppresses mTOR/NF-κB signaling in colorectal cancer [PMID:41522336]. TTC7B also binds Chikungunya virus nsP2 and contributes to nsP2-induced host cell shutoff [PMID:22258240].","teleology":[{"year":2012,"claim":"Established a first cellular role for TTC7B by identifying it as a host interactor of a viral protein, linking it to virus-induced host shutoff before its core biochemistry was known.","evidence":"High-throughput yeast two-hybrid with protein complementation assay validation and siRNA knockdown luciferase reporter assays for Chikungunya nsP2","pmids":["22258240"],"confidence":"Medium","gaps":["Mechanism downstream of the TTC7B-nsP2 interaction not resolved","No connection to PI4KA biology made at this stage","Single-study interaction without reciprocal endogenous validation"]},{"year":2021,"claim":"Placed TTC7B within a defined plasma membrane PI4KA complex and showed the complex is dynamically regulated, answering how PI4P production is controlled during GPCR signaling.","evidence":"HDX-MS, Co-IP, calcineurin substrate identification, PI4P production assay, and palmitoylation experiments","pmids":["34663815"],"confidence":"High","gaps":["TTC7B's own contribution to catalysis vs. scaffolding not separated","Direct TTC7B contacts within the complex not mapped at residue level"]},{"year":2024,"claim":"Resolved the structural basis for complex assembly, showing how the EFR3A C-terminus engages TTC7B and FAM126A to recruit PI4KA to the membrane.","evidence":"Cryo-EM structure of the EFR3A C-terminus bound to PI4KA-TTC7B-FAM126A with HDX-MS and mutational plasma-membrane recruitment assays","pmids":["39705356","38746453"],"confidence":"High","gaps":["Does not define isoform-specific differences among EFR3/TTC7/FAM126 paralogs","Dynamics of complex assembly in live cells not captured"]},{"year":2025,"claim":"Quantified the determinants of complex specificity and demonstrated that targeting the EFR3-TTC7B interface is sufficient to inhibit PI4KA activity, defining TTC7B as a druggable node.","evidence":"Yeast-display nanobody selection, cryo-EM, HDX-MS, reconstituted lipid bilayer and cellular PI4P assays, and binding affinity measurements","pmids":["41197736","41473329"],"confidence":"High","gaps":["Physiological consequence of high EFR3A-TTC7B-FAM126A affinity preference not tested in tissue","Phosphoregulation of EFR3B binding not linked to an upstream kinase"]},{"year":2025,"claim":"Connected TTC7B's PI4KA scaffolding role to AKT-dependent transcriptional programs, but revealed opposing tumor phenotypes depending on context.","evidence":"Cancer cell lines and xenografts with TTC7B knockdown/overexpression, AKT inhibition, RXRA promoter binding, m6A quantification, FTO ablation (colon), and JKAMP epistasis with IGF-1 rescue (head and neck)","pmids":["39897037","41392613"],"confidence":"Medium","gaps":["Biochemical link between PI4KA binding and AKT activation not directly reconstituted","Why TTC7B-AKT signaling is antiproliferative in colon but pro-invasive in head and neck cancer is unexplained","Single-lab functional data per cancer type"]},{"year":2026,"claim":"Identified how TTC7B protein abundance is set, showing TRIM21-mediated ubiquitination is antagonized by GIPC1 to control downstream mTOR/NF-κB signaling.","evidence":"Ubiquitination assays, TRIM21 E3 ligase knockdown, GIPC1 manipulation, in vitro functional assays, and in vivo tumor models with GIPC1 nanoparticles plus 5-FU","pmids":["41522336"],"confidence":"Medium","gaps":["Direct TRIM21-TTC7B ubiquitination site not mapped","Whether stability control intersects the PI4KA complex assembly is unknown","Single-lab study"]},{"year":null,"claim":"How TTC7B's structurally defined PI4KA-scaffolding function mechanistically produces its divergent AKT/mTOR/NF-κB signaling outputs across tissues remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No direct biochemical chain linking PI4P production to AKT activation by TTC7B","Context-dependence of pro- vs. anti-tumor effects unexplained","Regulatory crosstalk between ubiquitination, phosphoregulation, and complex assembly not integrated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,2]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1,2]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,4,6]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[4,5,6]}],"complexes":["PI4KA-TTC7B-FAM126A-EFR3 plasma membrane complex"],"partners":["PI4KA","FAM126A","EFR3A","EFR3B","TRIM21","GIPC1","NSP2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86TV6","full_name":"Tetratricopeptide repeat protein 7B","aliases":["Tetratricopeptide repeat protein 7-like-1","TPR repeat protein 7-like-1"],"length_aa":843,"mass_kda":94.2,"function":"Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane. The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis. In the complex, plays a central role in bridging PI4KA to EFR3B and HYCC1, via direct interactions (PubMed:26571211)","subcellular_location":"Cytoplasm, cytosol; Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q86TV6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TTC7B","classification":"Not Classified","n_dependent_lines":8,"n_total_lines":1208,"dependency_fraction":0.006622516556291391},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PI4KA","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/TTC7B","total_profiled":1310},"omim":[{"mim_id":"620060","title":"TETRATRICOPEPTIDE REPEAT DOMAIN-CONTAINING PROTEIN 7B; TTC7B","url":"https://www.omim.org/entry/620060"},{"mim_id":"616797","title":"EFR3 HOMOLOG B; EFR3B","url":"https://www.omim.org/entry/616797"},{"mim_id":"616757","title":"TRANSMEMBRANE PROTEIN 150A; TMEM150A","url":"https://www.omim.org/entry/616757"},{"mim_id":"611798","title":"EFR3 HOMOLOG A; EFR3A","url":"https://www.omim.org/entry/611798"},{"mim_id":"610531","title":"HYCCIN, PI4KA LIPID KINASE COMPLEX, SUBUNIT 1; HYCC1","url":"https://www.omim.org/entry/610531"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"brain","ntpm":105.9}],"url":"https://www.proteinatlas.org/search/TTC7B"},"hgnc":{"alias_symbol":[],"prev_symbol":["TTC7L1"]},"alphafold":{"accession":"Q86TV6","domains":[{"cath_id":"1.25.40","chopping":"10-124","consensus_level":"medium","plddt":87.2088,"start":10,"end":124}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86TV6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86TV6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86TV6-F1-predicted_aligned_error_v6.png","plddt_mean":85.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TTC7B","jax_strain_url":"https://www.jax.org/strain/search?query=TTC7B"},"sequence":{"accession":"Q86TV6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86TV6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86TV6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86TV6"}},"corpus_meta":[{"pmid":"22453632","id":"PMC_22453632","title":"TTC7B emerges as a novel risk factor for ischemic stroke through the convergence of several genome-wide approaches.","date":"2012","source":"Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/22453632","citation_count":110,"is_preprint":false},{"pmid":"22258240","id":"PMC_22258240","title":"Mapping of Chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component.","date":"2012","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/22258240","citation_count":97,"is_preprint":false},{"pmid":"26057119","id":"PMC_26057119","title":"Epigenetic age signatures in the forensically relevant body fluid of semen: a preliminary study.","date":"2015","source":"Forensic science international. Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26057119","citation_count":95,"is_preprint":false},{"pmid":"21915269","id":"PMC_21915269","title":"A stratified transcriptomics analysis of polygenic fat and lean mouse adipose tissues identifies novel candidate obesity genes.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21915269","citation_count":49,"is_preprint":false},{"pmid":"34663815","id":"PMC_34663815","title":"Palmitoylation targets the calcineurin phosphatase to the phosphatidylinositol 4-kinase complex at the plasma membrane.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34663815","citation_count":42,"is_preprint":false},{"pmid":"29413993","id":"PMC_29413993","title":"A validation study of DNA methylation-based age prediction using semen in forensic casework samples.","date":"2018","source":"Legal medicine (Tokyo, Japan)","url":"https://pubmed.ncbi.nlm.nih.gov/29413993","citation_count":33,"is_preprint":false},{"pmid":"39705356","id":"PMC_39705356","title":"Molecular basis for plasma membrane recruitment of PI4KA by EFR3.","date":"2024","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/39705356","citation_count":13,"is_preprint":false},{"pmid":"30983012","id":"PMC_30983012","title":"Genome-wide association studies for milk production traits in Valle del Belice sheep using repeated measures.","date":"2019","source":"Animal genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30983012","citation_count":11,"is_preprint":false},{"pmid":"38488745","id":"PMC_38488745","title":"Strategies to deal with genetic analyzer-specific DNA methylation measurements.","date":"2024","source":"Electrophoresis","url":"https://pubmed.ncbi.nlm.nih.gov/38488745","citation_count":8,"is_preprint":false},{"pmid":"33634591","id":"PMC_33634591","title":"14q32.11 microdeletion including CALM1, TTC7B, PSMC1, and RPS6KA5: A new potential cause of developmental and language delay in three unrelated patients.","date":"2021","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/33634591","citation_count":7,"is_preprint":false},{"pmid":"39897037","id":"PMC_39897037","title":"TTC7B triggers the PI4KA-AKT1-RXRA-FTO axis and inhibits colon cancer cell proliferation by increasing RNA methylation.","date":"2025","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39897037","citation_count":5,"is_preprint":false},{"pmid":"39162072","id":"PMC_39162072","title":"A semen-specific deoxyribonucleic acid methylation model for epigenetic age estimation and its robustness under environmental challenges.","date":"2024","source":"Electrophoresis","url":"https://pubmed.ncbi.nlm.nih.gov/39162072","citation_count":3,"is_preprint":false},{"pmid":"39634417","id":"PMC_39634417","title":"Novel bioinformatic approaches show the role of driver genes in the progression of cervical cancer: An in-silico study.","date":"2024","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/39634417","citation_count":2,"is_preprint":false},{"pmid":"41522336","id":"PMC_41522336","title":"GIPC1 Restrains the Progression and Chemoresistance of Colorectal Cancer by Regulating TTC7B/mTOR/NF-κB Axis.","date":"2026","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41522336","citation_count":1,"is_preprint":false},{"pmid":"38746453","id":"PMC_38746453","title":"Molecular basis for plasma membrane recruitment of PI4KA by EFR3.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38746453","citation_count":1,"is_preprint":false},{"pmid":"41197736","id":"PMC_41197736","title":"Development of an inhibitory TTC7B selective nanobody that blocks EFR3 recruitment of PI4KA.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41197736","citation_count":0,"is_preprint":false},{"pmid":"41473329","id":"PMC_41473329","title":"Development of an inhibitory TTC7B selective nanobody that blocks EFR3 recruitment of PI4KA.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41473329","citation_count":0,"is_preprint":false},{"pmid":"41392613","id":"PMC_41392613","title":"TTC7B Activates the AKT-JKAMP Signaling Axis to Promote Tumor Progression in Head and Neck Cancer.","date":"2025","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/41392613","citation_count":0,"is_preprint":false},{"pmid":"42156840","id":"PMC_42156840","title":"Genetic determinants of drug-induced gingival overgrowth.","date":"2026","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/42156840","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11449,"output_tokens":2156,"usd":0.033343,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9156,"output_tokens":2886,"usd":0.058965,"stage2_stop_reason":"end_turn"},"total_usd":0.092308,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"TTC7B is a component of the plasma membrane-localized phosphatidylinositol 4-kinase (PI4KA) complex, which also contains EFR3B, PI4KA, and FAM126A. Palmitoylated CNAβ1 (calcineurin isoform) was shown to interact with this complex, and calcineurin was identified to dephosphorylate FAM126A, promoting PI4KA complex activity and PI4P production during Gq-coupled GPCR signaling.\",\n      \"method\": \"Hydrogen-deuterium exchange mass spectrometry, Co-immunoprecipitation, calcineurin substrate identification, phosphatidylinositol 4-phosphate production assay, palmitoylation/depalmitoylation experiments\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — HDX-MS plus reciprocal interaction mapping, substrate phosphorylation assay, and functional PI4P production readout in a single study\",\n      \"pmids\": [\"34663815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structure of EFR3A C-terminus bound to the PI4KA-TTC7B-FAM126A complex revealed that the EFR3A C-terminus undergoes a disorder-to-order transition upon binding, making direct contacts with both TTC7B and FAM126A. Complex-disrupting mutations in TTC7B, FAM126A, and EFR3 decrease PI4KA recruitment to the plasma membrane.\",\n      \"method\": \"Cryo-electron microscopy (cryo-EM), hydrogen-deuterium exchange mass spectrometry (HDX-MS), mutational analysis, plasma membrane recruitment assay\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution cryo-EM structure with HDX-MS validation and mutational functional analysis; replicated in preprint (PMID:38746453)\",\n      \"pmids\": [\"39705356\", \"38746453\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A TTC7B-selective nanobody was developed that sterically blocks EFR3 binding to TTC7B-containing PI4KA complexes. Cryo-EM and HDX-MS showed the nanobody forms an extended interface with both PI4KA and TTC7B. The nanobody caused decreased PI4KA membrane recruitment on lipid bilayers and in cells, with reduced plasma membrane PI4P production. EFR3A-TTC7B-FAM126A binds with ~10-fold higher affinity than most other EFR3-TTC7-FAM126 combinations, and EFR3B phosphorylation markedly decreases binding to TTC7-FAM126.\",\n      \"method\": \"Yeast display nanobody selection, cryo-EM, HDX-MS, lipid bilayer reconstitution assay, cellular PI4P production assay, binding affinity measurements\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure, HDX-MS, reconstituted lipid bilayer assay, and cellular readouts in single study; preprint version also available (PMID:41473329)\",\n      \"pmids\": [\"41197736\", \"41473329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"TTC7B (tetratricopeptide repeat protein 7B) was identified as a binding partner of Chikungunya virus nonstructural protein nsP2 by yeast two-hybrid assay, and gene silencing experiments showed TTC7B plays a significant role in nsP2-induced cellular shutoff activity.\",\n      \"method\": \"High-throughput yeast two-hybrid (HT-Y2H), protein complementation assay (PCA), gene silencing with luciferase reporter assay\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — Y2H interaction validated by PCA and siRNA knockdown in a single study, but functional mechanism downstream of TTC7B-nsP2 interaction not fully resolved\",\n      \"pmids\": [\"22258240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TTC7B activates AKT1 signaling (via its role as a PI4KA-binding protein), which upregulates RXRA expression. RXRA acts as a transcription factor for the FTO gene, increasing FTO expression and decreasing total RNA m6A modification. TTC7B inhibited colon cancer cell proliferation through this PI4KA-AKT1-RXRA-FTO axis; ablation of FTO demethylase activity abolished TTC7B's antiproliferative effect in vitro and in vivo.\",\n      \"method\": \"Biological experiments in colon cancer cell lines and xenografts, transcription factor binding assay (RXRA recruitment to FTO promoter), m6A quantification, FTO activity ablation, in vivo tumor models\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — multiple functional assays and in vivo data from a single lab, but mechanistic links between PI4KA binding and AKT1 activation by TTC7B not directly biochemically resolved\",\n      \"pmids\": [\"39897037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"GIPC1 reduces ubiquitination of TTC7B by downregulating the E3 ubiquitin ligase TRIM21, thereby stabilizing TTC7B protein expression. Stabilized TTC7B in turn inhibits downstream mTOR/NF-κB signaling, suppressing colorectal cancer cell proliferation, migration, invasion, and chemoresistance.\",\n      \"method\": \"Ubiquitination assay, E3 ligase knockdown, in vitro functional assays (proliferation, migration, invasion), in vivo tumor models, GIPC1-loaded lipid nanoparticles combined with 5-FU\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — ubiquitination assay identifies TRIM21 as TTC7B E3 ligase with in vivo validation, but all from a single lab\",\n      \"pmids\": [\"41522336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TTC7B promotes head and neck cancer (HNC) cell migration and invasion through activation of AKT, which upregulates JKAMP. Pharmacological AKT inhibition abolished TTC7B-induced AKT phosphorylation and JKAMP expression, suppressing migration and invasion. IGF-1-mediated AKT activation rescued TTC7B-knockdown phenotypes, and JKAMP silencing in TTC7B-overexpressing cells reduced migration and invasion.\",\n      \"method\": \"In vitro migration/invasion assays, TTC7B knockdown and overexpression, AKT pharmacological inhibition, IGF-1 stimulation rescue experiments, JKAMP silencing\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — multiple epistasis-style rescue experiments in cell lines from a single lab; no direct biochemical reconstitution of TTC7B-AKT interaction\",\n      \"pmids\": [\"41392613\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TTC7B is a scaffold protein that forms a stable heterotrimeric complex with PI4KA and FAM126, recruited to the plasma membrane by EFR3A/B; structural and mutational studies show TTC7B directly contacts EFR3 to position PI4KA for phosphatidylinositol 4-phosphate production, while additional studies indicate TTC7B modulates AKT/mTOR/NF-κB signaling and is itself regulated by TRIM21-mediated ubiquitination, and its stability and activity are further controlled by calcineurin-mediated dephosphorylation of the complex.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TTC7B is a scaffold subunit of the plasma membrane phosphatidylinositol 4-kinase (PI4KA) complex, where it bridges the catalytic kinase PI4KA, FAM126A, and the membrane anchor EFR3 to drive phosphatidylinositol 4-phosphate (PI4P) production [#0, #1]. Cryo-EM and HDX-MS analyses show that the EFR3A C-terminus undergoes a disorder-to-order transition upon binding and makes direct contacts with both TTC7B and FAM126A, and that complex-disrupting mutations in TTC7B reduce PI4KA recruitment to the plasma membrane [#1]; the EFR3A-TTC7B-FAM126A combination binds with ~10-fold higher affinity than most other EFR3-TTC7-FAM126 pairings, and sterically blocking the EFR3-TTC7B interface with a selective nanobody decreases PI4KA membrane recruitment and PI4P production [#2]. Assembly and activity of the complex are dynamically regulated: calcineurin dephosphorylates FAM126A to promote PI4KA activity and PI4P production during Gq-coupled GPCR signaling, while EFR3B phosphorylation markedly weakens binding to TTC7-FAM126 [#0, #2]. Through its PI4KA-linked role, TTC7B modulates AKT signaling with context-dependent outcomes in cancer: it activates a PI4KA-AKT1-RXRA-FTO axis that lowers RNA m6A and suppresses colon cancer proliferation [#4], yet activates AKT-dependent JKAMP induction that promotes head and neck cancer migration and invasion [#6]. TTC7B protein levels are controlled by TRIM21-mediated ubiquitination, which is antagonized by GIPC1, and stabilized TTC7B suppresses mTOR/NF-\\u03baB signaling in colorectal cancer [#5]. TTC7B also binds Chikungunya virus nsP2 and contributes to nsP2-induced host cell shutoff [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established a first cellular role for TTC7B by identifying it as a host interactor of a viral protein, linking it to virus-induced host shutoff before its core biochemistry was known.\",\n      \"evidence\": \"High-throughput yeast two-hybrid with protein complementation assay validation and siRNA knockdown luciferase reporter assays for Chikungunya nsP2\",\n      \"pmids\": [\"22258240\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism downstream of the TTC7B-nsP2 interaction not resolved\", \"No connection to PI4KA biology made at this stage\", \"Single-study interaction without reciprocal endogenous validation\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Placed TTC7B within a defined plasma membrane PI4KA complex and showed the complex is dynamically regulated, answering how PI4P production is controlled during GPCR signaling.\",\n      \"evidence\": \"HDX-MS, Co-IP, calcineurin substrate identification, PI4P production assay, and palmitoylation experiments\",\n      \"pmids\": [\"34663815\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"TTC7B's own contribution to catalysis vs. scaffolding not separated\", \"Direct TTC7B contacts within the complex not mapped at residue level\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved the structural basis for complex assembly, showing how the EFR3A C-terminus engages TTC7B and FAM126A to recruit PI4KA to the membrane.\",\n      \"evidence\": \"Cryo-EM structure of the EFR3A C-terminus bound to PI4KA-TTC7B-FAM126A with HDX-MS and mutational plasma-membrane recruitment assays\",\n      \"pmids\": [\"39705356\", \"38746453\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define isoform-specific differences among EFR3/TTC7/FAM126 paralogs\", \"Dynamics of complex assembly in live cells not captured\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Quantified the determinants of complex specificity and demonstrated that targeting the EFR3-TTC7B interface is sufficient to inhibit PI4KA activity, defining TTC7B as a druggable node.\",\n      \"evidence\": \"Yeast-display nanobody selection, cryo-EM, HDX-MS, reconstituted lipid bilayer and cellular PI4P assays, and binding affinity measurements\",\n      \"pmids\": [\"41197736\", \"41473329\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological consequence of high EFR3A-TTC7B-FAM126A affinity preference not tested in tissue\", \"Phosphoregulation of EFR3B binding not linked to an upstream kinase\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected TTC7B's PI4KA scaffolding role to AKT-dependent transcriptional programs, but revealed opposing tumor phenotypes depending on context.\",\n      \"evidence\": \"Cancer cell lines and xenografts with TTC7B knockdown/overexpression, AKT inhibition, RXRA promoter binding, m6A quantification, FTO ablation (colon), and JKAMP epistasis with IGF-1 rescue (head and neck)\",\n      \"pmids\": [\"39897037\", \"41392613\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Biochemical link between PI4KA binding and AKT activation not directly reconstituted\", \"Why TTC7B-AKT signaling is antiproliferative in colon but pro-invasive in head and neck cancer is unexplained\", \"Single-lab functional data per cancer type\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified how TTC7B protein abundance is set, showing TRIM21-mediated ubiquitination is antagonized by GIPC1 to control downstream mTOR/NF-\\u03baB signaling.\",\n      \"evidence\": \"Ubiquitination assays, TRIM21 E3 ligase knockdown, GIPC1 manipulation, in vitro functional assays, and in vivo tumor models with GIPC1 nanoparticles plus 5-FU\",\n      \"pmids\": [\"41522336\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct TRIM21-TTC7B ubiquitination site not mapped\", \"Whether stability control intersects the PI4KA complex assembly is unknown\", \"Single-lab study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TTC7B's structurally defined PI4KA-scaffolding function mechanistically produces its divergent AKT/mTOR/NF-\\u03baB signaling outputs across tissues remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct biochemical chain linking PI4P production to AKT activation by TTC7B\", \"Context-dependence of pro- vs. anti-tumor effects unexplained\", \"Regulatory crosstalk between ubiquitination, phosphoregulation, and complex assembly not integrated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 4, 6]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [4, 5, 6]}\n    ],\n    \"complexes\": [\"PI4KA-TTC7B-FAM126A-EFR3 plasma membrane complex\"],\n    \"partners\": [\"PI4KA\", \"FAM126A\", \"EFR3A\", \"EFR3B\", \"TRIM21\", \"GIPC1\", \"nsP2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":6,"faith_total":6,"faith_pct":100.0}}