{"gene":"LTBR","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2022,"finding":"CREB1 directly binds the LTBR promoter and transcriptionally activates LTBR expression, as confirmed by luciferase reporter assay and ChIP assay. LTBR in turn regulates the NF-κB pathway to modulate lung epithelial cell viability and apoptosis.","method":"Luciferase reporter assay, ChIP assay, siRNA knockdown, cell viability (CCK-8), flow cytometry apoptosis analysis","journal":"Computational and mathematical methods in medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase reporter and ChIP confirm direct transcriptional activation; NF-κB pathway modulation confirmed by silencing; single lab with two orthogonal methods","pmids":["36118831"],"is_preprint":false},{"year":2024,"finding":"LTBR maintains the immunosuppressive activity and M2 phenotype of tumor-associated macrophages via noncanonical NF-κB and Wnt/β-catenin signaling pathways; macrophage-specific knockout of LTBR blocks TAM immunosuppressive activity and M2 polarization.","method":"Macrophage-specific LTBR knockout mouse model, tumor growth assays, immune phenotyping (CD8+ T cells, myeloid-derived suppressor cells), siRNA-mediated knockdown in TAMs","journal":"iMeta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — macrophage-specific KO with defined cellular phenotype and pathway identification; single lab, multiple readouts","pmids":["39429877"],"is_preprint":false},{"year":2024,"finding":"LTα1/β2 ligand activates the LTBR/NIK/RelB (non-canonical NF-κB) signaling axis, promoting proliferation in cholangiocarcinoma cell lines and patient-derived organoids; NIK inhibition suppresses RelB expression and nuclear co-translocation of RelB and p52.","method":"CCA cell lines and patient-derived organoids, real-time impedance measurement, flow cytometry, immunoblot, qRT-PCR, RNA sequencing, in vivo murine CCA models","journal":"Liver international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (in vitro + in vivo) in single lab establishing LTBR→NIK→RelB axis","pmids":["39164890"],"is_preprint":false},{"year":2023,"finding":"TRAF5 physically interacts with LTBR (confirmed by co-immunoprecipitation and immunofluorescence); TRAF5 silencing downregulates LTBR expression and suppresses LTBR-mediated NF-κB signaling, enhancing necroptosis in hepatocellular carcinoma cells. LTBR overexpression rescues proliferation, migration, and invasion and abolishes the pro-necroptotic effect of TRAF5 knockdown.","method":"Co-immunoprecipitation, immunofluorescence, siRNA knockdown and overexpression, CCK-8, colony formation, Transwell, flow cytometry, Hoechst/PI staining, xenograft tumor model, western blotting","journal":"PeerJ","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP confirms TRAF5-LTBR interaction; functional rescue experiments and in vivo validation in single lab","pmids":["37366426"],"is_preprint":false},{"year":2026,"finding":"Targeted agonistic activation of LTβR signaling on FAP-expressing tumor stroma drives high endothelial venule (HEV) differentiation, induces chemokine secretion from endothelial cells, enhances T cell adhesion and extravasation, and promotes formation of TLS-like immune aggregates in the tumor microenvironment.","method":"FAP-LTBR bispecific agonist in vitro (primary human endothelial cells, 3D microfluidic vascular models) and in vivo (multiple murine tumor models), spatial transcriptomics, 3D immunophenotyping","journal":"Clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple in vitro and in vivo models with functional readouts; single lab with orthogonal methods","pmids":["42012453"],"is_preprint":false},{"year":2025,"finding":"LTβR signaling in cancer cells, together with IFN sensing, is necessary and sufficient for CD8+ TIL-mediated, class I HLA-independent cancer cell lysis, as identified by whole-genome loss-of-function CRISPR screen and confirmed by validation studies; expanded CD8+ TIL express high LTB and upregulate LTA upon co-culture with cancer cells.","method":"Whole-genome CRISPR loss-of-function screen, patient-derived TIL-melanoma co-cultures, paired scRNA-seq and scTCR-seq, functional validation assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide CRISPR screen with functional validation in patient-derived co-cultures; single lab, preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.11.19.689204"],"is_preprint":true},{"year":2013,"finding":"Recombinant rabbit (Oryctolagus cuniculus) soluble TNFSF14 and extracellular LTBR proteins were produced and shown to bind splenic T cells in vitro, confirming direct protein-protein binding between TNFSF14 (LIGHT) and LTBR.","method":"Recombinant protein expression, Ni-NTA affinity purification, confocal laser microscopy binding assay with splenic T cells","journal":"Molecular immunology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single binding assay in rabbit ortholog model, no functional pathway dissection or mutagenesis; single lab","pmids":["23370464"],"is_preprint":false}],"current_model":"LTBR (lymphotoxin-β receptor) is a TNF receptor superfamily member that, upon binding LTα1/β2 or LIGHT (TNFSF14), activates both canonical and non-canonical NF-κB signaling (via NIK→RelB) and Wnt/β-catenin pathways; it physically associates with TRAF5, whose expression sustains LTBR levels; its transcription is directly activated by CREB1; and in the tumor microenvironment it controls macrophage M2 polarization, endothelial HEV differentiation, TLS formation, and, in cancer cells, serves as a necessary co-receptor (with IFN sensing) for CD8+ TIL-mediated HLA-independent cytotoxicity."},"narrative":{"mechanistic_narrative":"LTBR is a TNF receptor superfamily member that transduces lymphotoxin/LIGHT signals into NF-κB activation to shape immune cell behavior and the tumor microenvironment [PMID:39164890, PMID:23370464]. Upon engagement by its LTα1/β2 ligand, LTBR drives the non-canonical NF-κB axis through NIK and RelB, where NIK inhibition abrogates RelB expression and nuclear co-translocation of RelB and p52, promoting tumor cell proliferation [PMID:39164890]. Receptor abundance and signaling output are stabilized by physical association with TRAF5, whose loss downregulates LTBR and suppresses LTBR-driven NF-κB signaling [PMID:37366426], while LTBR transcription is directly activated by CREB1 binding at its promoter [PMID:36118831]. Through non-canonical NF-κB together with Wnt/β-catenin signaling, LTBR sustains the immunosuppressive M2 phenotype of tumor-associated macrophages [PMID:39429877], and agonistic activation of the receptor on tumor stroma drives high endothelial venule differentiation and tertiary lymphoid structure formation that enhance T cell adhesion and extravasation [PMID:42012453]. In cancer cells, LTBR signaling acts alongside IFN sensing as a necessary determinant of CD8+ TIL-mediated, HLA class I-independent cytotoxicity [PMID:bio_10.1101_2025.11.19.689204].","teleology":[{"year":2013,"claim":"Established that LTBR directly binds its ligand TNFSF14 (LIGHT) at the protein level, anchoring it as a functional receptor for this ligand.","evidence":"Recombinant soluble TNFSF14 and extracellular LTBR proteins in a confocal binding assay with rabbit splenic T cells","pmids":["23370464"],"confidence":"Low","gaps":["Binding shown only in rabbit ortholog without mutagenesis","No downstream signaling or affinity quantification","Does not address LTα1/β2 ligand binding"]},{"year":2022,"claim":"Identified the upstream transcriptional control of LTBR, showing CREB1 directly activates its promoter and that LTBR in turn modulates NF-κB-dependent epithelial viability.","evidence":"Luciferase reporter and ChIP assays with siRNA knockdown in lung epithelial cells","pmids":["36118831"],"confidence":"Medium","gaps":["NF-κB branch (canonical vs non-canonical) not resolved","Single lab","Physiological context of CREB1→LTBR axis unclear"]},{"year":2023,"claim":"Defined TRAF5 as a physical partner that stabilizes LTBR and its NF-κB output, linking receptor levels to a pro-survival, anti-necroptotic program.","evidence":"Reciprocal Co-IP, immunofluorescence, knockdown/overexpression rescue, and xenograft in hepatocellular carcinoma cells","pmids":["37366426"],"confidence":"Medium","gaps":["Mechanism by which TRAF5 sustains LTBR expression not defined","Direct binding interface not mapped","Single lab"]},{"year":2024,"claim":"Resolved the core signaling axis, demonstrating that LTα1/β2-LTBR engages NIK→RelB non-canonical NF-κB to drive proliferation.","evidence":"Cholangiocarcinoma cell lines and patient-derived organoids with NIK inhibition, immunoblot, RNA-seq, and in vivo murine models","pmids":["39164890"],"confidence":"Medium","gaps":["Relative contribution of canonical NF-κB not quantified","Single tumor type focus","Single lab"]},{"year":2024,"claim":"Established LTBR as a cell-intrinsic driver of tumor-associated macrophage immunosuppression and M2 polarization through non-canonical NF-κB and Wnt/β-catenin.","evidence":"Macrophage-specific LTBR knockout mice with tumor growth, immune phenotyping, and TAM knockdown","pmids":["39429877"],"confidence":"Medium","gaps":["How Wnt/β-catenin is engaged downstream of LTBR unresolved","Ligand source in TME not identified","Single lab"]},{"year":2026,"claim":"Showed that agonistic LTBR activation on tumor stroma reprograms the vasculature toward HEV differentiation and TLS formation, enhancing T cell infiltration.","evidence":"FAP-LTBR bispecific agonist in primary endothelial cells, 3D microfluidic models, and multiple murine tumor models with spatial transcriptomics","pmids":["42012453"],"confidence":"Medium","gaps":["Signaling branch mediating HEV differentiation not dissected","Durability of TLS-like aggregates unknown","Single lab"]},{"year":2025,"claim":"Implicated LTBR signaling in cancer cells, with IFN sensing, as a necessary co-determinant of HLA-independent CD8+ TIL cytotoxicity, defining a non-classical killing pathway.","evidence":"Whole-genome CRISPR loss-of-function screen and patient-derived TIL-melanoma co-cultures with paired scRNA-seq/scTCR-seq (preprint)","pmids":["bio_10.1101_2025.11.19.689204"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Molecular link between LTBR signaling and lysis sensitivity unresolved","Ligand source from TIL (LTA/LTB) interaction with cancer-cell LTBR not formally demonstrated"]},{"year":null,"claim":"How LTBR's distinct downstream branches (non-canonical NF-κB, Wnt/β-catenin) are selectively engaged in different cell types and ligand contexts remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of ligand-receptor-TRAF assembly in the corpus","Branch selection determinants unknown","Integration of IFN and LTBR signals mechanistically undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[2,6]},{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[6]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,0]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[1,4,5]}],"complexes":[],"partners":["TRAF5","TNFSF14","NIK","RELB"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P36941","full_name":"Tumor necrosis factor receptor superfamily member 3","aliases":["Lymphotoxin-beta receptor","Tumor necrosis factor C receptor","Tumor necrosis factor receptor 2-related protein","Tumor necrosis factor receptor type III","TNF-RIII","TNFR-III"],"length_aa":435,"mass_kda":46.7,"function":"Receptor for the heterotrimeric lymphotoxin containing LTA and LTB, and for TNFS14/LIGHT (PubMed:24248355). Activates NF-kappa-B signaling pathway upon stimulation with lymphotoxin (LTA(1)-LTB(2)) (PubMed:24248355). Promotes apoptosis via TRAF3 and TRAF5. May play a role in the development of lymphoid organs","subcellular_location":"Membrane","url":"https://www.uniprot.org/uniprotkb/P36941/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LTBR","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/LTBR","total_profiled":1310},"omim":[{"mim_id":"619289","title":"ZINC FINGER PROTEIN 91, ATYPICAL E3 UBIQUITIN LIGASE; ZFP91","url":"https://www.omim.org/entry/619289"},{"mim_id":"611211","title":"RECEPTOR EXPRESSED IN LYMPHOID TISSUES; RELT","url":"https://www.omim.org/entry/611211"},{"mim_id":"610562","title":"ZINC FINGER CCCH DOMAIN-CONTAINING PROTEIN 12A; ZC3H12A","url":"https://www.omim.org/entry/610562"},{"mim_id":"607414","title":"FEZ FAMILY ZINC FINGER PROTEIN 2; FEZF2","url":"https://www.omim.org/entry/607414"},{"mim_id":"607358","title":"AUTOIMMUNE REGULATOR; AIRE","url":"https://www.omim.org/entry/607358"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Golgi apparatus","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/LTBR"},"hgnc":{"alias_symbol":["TNFCR","TNFR-RP","TNFR2-RP","TNF-R-III","TNFRSF3"],"prev_symbol":["D12S370"]},"alphafold":{"accession":"P36941","domains":[{"cath_id":"2.10.50.10","chopping":"33-101","consensus_level":"medium","plddt":94.8499,"start":33,"end":101},{"cath_id":"2.10.50.10","chopping":"103-145","consensus_level":"medium","plddt":84.643,"start":103,"end":145},{"cath_id":"2.10.50.10","chopping":"148-215","consensus_level":"medium","plddt":84.9813,"start":148,"end":215}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P36941","model_url":"https://alphafold.ebi.ac.uk/files/AF-P36941-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P36941-F1-predicted_aligned_error_v6.png","plddt_mean":66.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LTBR","jax_strain_url":"https://www.jax.org/strain/search?query=LTBR"},"sequence":{"accession":"P36941","fasta_url":"https://rest.uniprot.org/uniprotkb/P36941.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P36941/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P36941"}},"corpus_meta":[{"pmid":"15811637","id":"PMC_15811637","title":"Muscle atrophy and bone loss after 90 days' bed rest and the effects of flywheel resistive exercise and pamidronate: results from the LTBR study.","date":"2005","source":"Bone","url":"https://pubmed.ncbi.nlm.nih.gov/15811637","citation_count":220,"is_preprint":false},{"pmid":"17259312","id":"PMC_17259312","title":"The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum.","date":"2007","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/17259312","citation_count":42,"is_preprint":false},{"pmid":"39429877","id":"PMC_39429877","title":"LTBR acts as a novel immune checkpoint of tumor-associated macrophages for cancer immunotherapy.","date":"2024","source":"iMeta","url":"https://pubmed.ncbi.nlm.nih.gov/39429877","citation_count":16,"is_preprint":false},{"pmid":"36118831","id":"PMC_36118831","title":"CREB1 Transcriptionally Activates LTBR to Promote the NF-κB Pathway and Apoptosis in Lung Epithelial Cells.","date":"2022","source":"Computational and mathematical methods in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/36118831","citation_count":10,"is_preprint":false},{"pmid":"39164890","id":"PMC_39164890","title":"Lymphotoxin beta-activated LTBR/NIK/RELB axis drives proliferation in cholangiocarcinoma.","date":"2024","source":"Liver international : official journal of the International Association for the Study of the Liver","url":"https://pubmed.ncbi.nlm.nih.gov/39164890","citation_count":8,"is_preprint":false},{"pmid":"28575727","id":"PMC_28575727","title":"Association of LTBR polymorphisms with chronic hepatitis B virus infection and hepatitis B virus-related hepatocellular carcinoma.","date":"2017","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/28575727","citation_count":8,"is_preprint":false},{"pmid":"37366426","id":"PMC_37366426","title":"Silencing of TRAF5 enhances necroptosis in hepatocellular carcinoma by inhibiting LTBR-mediated NF-κB signaling.","date":"2023","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/37366426","citation_count":6,"is_preprint":false},{"pmid":"38599071","id":"PMC_38599071","title":"Comprehensive analysis reveals that LTBR is a immune-related biomarker for glioma.","date":"2024","source":"Computers in biology and medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38599071","citation_count":4,"is_preprint":false},{"pmid":"23370464","id":"PMC_23370464","title":"Molecular characterization, expression and binding activity of the cytokines TNFSF14 and its receptor LTBR in Oryctolagus cuniculus (rabbit).","date":"2013","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/23370464","citation_count":3,"is_preprint":false},{"pmid":"42012453","id":"PMC_42012453","title":"FAP-Targeted LTBR Agonist Drives HEV Differentiation and Immune Niche Formation for Improved Immunotherapy Response in Solid Tumours.","date":"2026","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/42012453","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.19.689204","title":"Lymphotoxin-driven cancer cell eradication by tumoricidal CD8  <sup>+</sup>  TIL","date":"2025-11-19","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.19.689204","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.10.08.681192","title":"Causal Modeling Reveals Cell-Cell Communication Dynamics in the Tumor Microenvironment During Anti-PD-1 Therapy in Breast Cancer Patients","date":"2025-10-14","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.08.681192","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9448,"output_tokens":1926,"usd":0.028617,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8867,"output_tokens":2662,"usd":0.055442,"stage2_stop_reason":"end_turn"},"total_usd":0.084059,"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\": 2022,\n      \"finding\": \"CREB1 directly binds the LTBR promoter and transcriptionally activates LTBR expression, as confirmed by luciferase reporter assay and ChIP assay. LTBR in turn regulates the NF-κB pathway to modulate lung epithelial cell viability and apoptosis.\",\n      \"method\": \"Luciferase reporter assay, ChIP assay, siRNA knockdown, cell viability (CCK-8), flow cytometry apoptosis analysis\",\n      \"journal\": \"Computational and mathematical methods in medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase reporter and ChIP confirm direct transcriptional activation; NF-κB pathway modulation confirmed by silencing; single lab with two orthogonal methods\",\n      \"pmids\": [\"36118831\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LTBR maintains the immunosuppressive activity and M2 phenotype of tumor-associated macrophages via noncanonical NF-κB and Wnt/β-catenin signaling pathways; macrophage-specific knockout of LTBR blocks TAM immunosuppressive activity and M2 polarization.\",\n      \"method\": \"Macrophage-specific LTBR knockout mouse model, tumor growth assays, immune phenotyping (CD8+ T cells, myeloid-derived suppressor cells), siRNA-mediated knockdown in TAMs\",\n      \"journal\": \"iMeta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — macrophage-specific KO with defined cellular phenotype and pathway identification; single lab, multiple readouts\",\n      \"pmids\": [\"39429877\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LTα1/β2 ligand activates the LTBR/NIK/RelB (non-canonical NF-κB) signaling axis, promoting proliferation in cholangiocarcinoma cell lines and patient-derived organoids; NIK inhibition suppresses RelB expression and nuclear co-translocation of RelB and p52.\",\n      \"method\": \"CCA cell lines and patient-derived organoids, real-time impedance measurement, flow cytometry, immunoblot, qRT-PCR, RNA sequencing, in vivo murine CCA models\",\n      \"journal\": \"Liver international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (in vitro + in vivo) in single lab establishing LTBR→NIK→RelB axis\",\n      \"pmids\": [\"39164890\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRAF5 physically interacts with LTBR (confirmed by co-immunoprecipitation and immunofluorescence); TRAF5 silencing downregulates LTBR expression and suppresses LTBR-mediated NF-κB signaling, enhancing necroptosis in hepatocellular carcinoma cells. LTBR overexpression rescues proliferation, migration, and invasion and abolishes the pro-necroptotic effect of TRAF5 knockdown.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, siRNA knockdown and overexpression, CCK-8, colony formation, Transwell, flow cytometry, Hoechst/PI staining, xenograft tumor model, western blotting\",\n      \"journal\": \"PeerJ\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP confirms TRAF5-LTBR interaction; functional rescue experiments and in vivo validation in single lab\",\n      \"pmids\": [\"37366426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Targeted agonistic activation of LTβR signaling on FAP-expressing tumor stroma drives high endothelial venule (HEV) differentiation, induces chemokine secretion from endothelial cells, enhances T cell adhesion and extravasation, and promotes formation of TLS-like immune aggregates in the tumor microenvironment.\",\n      \"method\": \"FAP-LTBR bispecific agonist in vitro (primary human endothelial cells, 3D microfluidic vascular models) and in vivo (multiple murine tumor models), spatial transcriptomics, 3D immunophenotyping\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple in vitro and in vivo models with functional readouts; single lab with orthogonal methods\",\n      \"pmids\": [\"42012453\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LTβR signaling in cancer cells, together with IFN sensing, is necessary and sufficient for CD8+ TIL-mediated, class I HLA-independent cancer cell lysis, as identified by whole-genome loss-of-function CRISPR screen and confirmed by validation studies; expanded CD8+ TIL express high LTB and upregulate LTA upon co-culture with cancer cells.\",\n      \"method\": \"Whole-genome CRISPR loss-of-function screen, patient-derived TIL-melanoma co-cultures, paired scRNA-seq and scTCR-seq, functional validation assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide CRISPR screen with functional validation in patient-derived co-cultures; single lab, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.11.19.689204\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Recombinant rabbit (Oryctolagus cuniculus) soluble TNFSF14 and extracellular LTBR proteins were produced and shown to bind splenic T cells in vitro, confirming direct protein-protein binding between TNFSF14 (LIGHT) and LTBR.\",\n      \"method\": \"Recombinant protein expression, Ni-NTA affinity purification, confocal laser microscopy binding assay with splenic T cells\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single binding assay in rabbit ortholog model, no functional pathway dissection or mutagenesis; single lab\",\n      \"pmids\": [\"23370464\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LTBR (lymphotoxin-β receptor) is a TNF receptor superfamily member that, upon binding LTα1/β2 or LIGHT (TNFSF14), activates both canonical and non-canonical NF-κB signaling (via NIK→RelB) and Wnt/β-catenin pathways; it physically associates with TRAF5, whose expression sustains LTBR levels; its transcription is directly activated by CREB1; and in the tumor microenvironment it controls macrophage M2 polarization, endothelial HEV differentiation, TLS formation, and, in cancer cells, serves as a necessary co-receptor (with IFN sensing) for CD8+ TIL-mediated HLA-independent cytotoxicity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LTBR is a TNF receptor superfamily member that transduces lymphotoxin/LIGHT signals into NF-\\u03baB activation to shape immune cell behavior and the tumor microenvironment [#2, #6]. Upon engagement by its LT\\u03b11/\\u03b22 ligand, LTBR drives the non-canonical NF-\\u03baB axis through NIK and RelB, where NIK inhibition abrogates RelB expression and nuclear co-translocation of RelB and p52, promoting tumor cell proliferation [#2]. Receptor abundance and signaling output are stabilized by physical association with TRAF5, whose loss downregulates LTBR and suppresses LTBR-driven NF-\\u03baB signaling [#3], while LTBR transcription is directly activated by CREB1 binding at its promoter [#0]. Through non-canonical NF-\\u03baB together with Wnt/\\u03b2-catenin signaling, LTBR sustains the immunosuppressive M2 phenotype of tumor-associated macrophages [#1], and agonistic activation of the receptor on tumor stroma drives high endothelial venule differentiation and tertiary lymphoid structure formation that enhance T cell adhesion and extravasation [#4]. In cancer cells, LTBR signaling acts alongside IFN sensing as a necessary determinant of CD8+ TIL-mediated, HLA class I-independent cytotoxicity [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established that LTBR directly binds its ligand TNFSF14 (LIGHT) at the protein level, anchoring it as a functional receptor for this ligand.\",\n      \"evidence\": \"Recombinant soluble TNFSF14 and extracellular LTBR proteins in a confocal binding assay with rabbit splenic T cells\",\n      \"pmids\": [\"23370464\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Binding shown only in rabbit ortholog without mutagenesis\", \"No downstream signaling or affinity quantification\", \"Does not address LT\\u03b11/\\u03b22 ligand binding\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified the upstream transcriptional control of LTBR, showing CREB1 directly activates its promoter and that LTBR in turn modulates NF-\\u03baB-dependent epithelial viability.\",\n      \"evidence\": \"Luciferase reporter and ChIP assays with siRNA knockdown in lung epithelial cells\",\n      \"pmids\": [\"36118831\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"NF-\\u03baB branch (canonical vs non-canonical) not resolved\", \"Single lab\", \"Physiological context of CREB1\\u2192LTBR axis unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined TRAF5 as a physical partner that stabilizes LTBR and its NF-\\u03baB output, linking receptor levels to a pro-survival, anti-necroptotic program.\",\n      \"evidence\": \"Reciprocal Co-IP, immunofluorescence, knockdown/overexpression rescue, and xenograft in hepatocellular carcinoma cells\",\n      \"pmids\": [\"37366426\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which TRAF5 sustains LTBR expression not defined\", \"Direct binding interface not mapped\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved the core signaling axis, demonstrating that LT\\u03b11/\\u03b22-LTBR engages NIK\\u2192RelB non-canonical NF-\\u03baB to drive proliferation.\",\n      \"evidence\": \"Cholangiocarcinoma cell lines and patient-derived organoids with NIK inhibition, immunoblot, RNA-seq, and in vivo murine models\",\n      \"pmids\": [\"39164890\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relative contribution of canonical NF-\\u03baB not quantified\", \"Single tumor type focus\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established LTBR as a cell-intrinsic driver of tumor-associated macrophage immunosuppression and M2 polarization through non-canonical NF-\\u03baB and Wnt/\\u03b2-catenin.\",\n      \"evidence\": \"Macrophage-specific LTBR knockout mice with tumor growth, immune phenotyping, and TAM knockdown\",\n      \"pmids\": [\"39429877\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How Wnt/\\u03b2-catenin is engaged downstream of LTBR unresolved\", \"Ligand source in TME not identified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Showed that agonistic LTBR activation on tumor stroma reprograms the vasculature toward HEV differentiation and TLS formation, enhancing T cell infiltration.\",\n      \"evidence\": \"FAP-LTBR bispecific agonist in primary endothelial cells, 3D microfluidic models, and multiple murine tumor models with spatial transcriptomics\",\n      \"pmids\": [\"42012453\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signaling branch mediating HEV differentiation not dissected\", \"Durability of TLS-like aggregates unknown\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated LTBR signaling in cancer cells, with IFN sensing, as a necessary co-determinant of HLA-independent CD8+ TIL cytotoxicity, defining a non-classical killing pathway.\",\n      \"evidence\": \"Whole-genome CRISPR loss-of-function screen and patient-derived TIL-melanoma co-cultures with paired scRNA-seq/scTCR-seq (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.11.19.689204\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Molecular link between LTBR signaling and lysis sensitivity unresolved\", \"Ligand source from TIL (LTA/LTB) interaction with cancer-cell LTBR not formally demonstrated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How LTBR's distinct downstream branches (non-canonical NF-\\u03baB, Wnt/\\u03b2-catenin) are selectively engaged in different cell types and ligand contexts remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of ligand-receptor-TRAF assembly in the corpus\", \"Branch selection determinants unknown\", \"Integration of IFN and LTBR signals mechanistically undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 0]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [1, 4, 5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TRAF5\", \"TNFSF14\", \"NIK\", \"RelB\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":3,"faith_total":4,"faith_pct":75.0}}