{"gene":"ILDR2","run_date":"2026-06-10T01:55:23","timeline":{"discoveries":[{"year":2012,"finding":"ILDR2 localizes at tricellular contacts (TCs) in epithelial tissues and recruits tricellulin to tricellular tight junctions (tTJs), functioning as an 'angulin' family protein alongside LSR and ILDR1.","method":"Immunofluorescence localization in mouse epithelial tissues and cultured epithelial cells; functional tricellulin recruitment assay","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional consequence (tricellulin recruitment), multiple epithelial cell types and tissues examined, consistent with broader angulin family framework","pmids":["23239027"],"is_preprint":false},{"year":2012,"finding":"ILDR2 provides a much weaker epithelial barrier function compared to LSR and ILDR1 when introduced into cultured epithelial cells.","method":"Introduction of ILDR2 into cultured epithelial cells followed by barrier function assay","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, single functional assay in cultured cells showing weaker barrier relative to LSR/ILDR1","pmids":["23239027"],"is_preprint":false},{"year":2013,"finding":"ILDR2 is primarily located in the endoplasmic reticulum membrane in hepatoma and neuronal cells, and manipulation of hepatic ILDR2 expression (knockdown or overexpression via adenovirus) affects hepatic lipid homeostasis and ER stress pathway gene expression.","method":"Subcellular fractionation/ER localization in cell lines; adenoviral shRNA knockdown and CMV-driven overexpression in mouse liver; measurement of hepatic triglycerides, cholesterol, VLDL, and ER stress gene expression","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct ER localization plus gain- and loss-of-function in vivo with lipid and ER stress readouts; however, causal primacy between lipid effects and ER stress effects not resolved in this study","pmids":["23826244"],"is_preprint":false},{"year":2018,"finding":"ILDR2 negatively regulates T cell responses; an ILDR2 extracellular domain–Fc fusion protein binds to a putative counterpart on activated T cells and inhibits proinflammatory cytokine/chemokine production in autologous macrophage–T cell cocultures, and shows benefit in the collagen-induced arthritis model.","method":"ILDR2-Fc fusion protein binding assay on activated T cells; in vitro coculture cytokine inhibition assay; collagen-induced arthritis mouse model","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — binding assay plus in vitro functional assay plus in vivo disease model; single lab, receptor identity on T cells not yet fully defined","pmids":["29431694"],"is_preprint":false},{"year":2017,"finding":"ILDR2 binds to splicing factors TRA2A, TRA2B, and SRSF1, translocates into the nucleus when these splicing factors are present, and regulates alternative pre-mRNA splicing of TUBD1 and IQCB1; siRNA knockdown of endogenous ILDR2 in cultured cells affects alternative splicing of these targets.","method":"Co-immunoprecipitation/pulldown with splicing factors; nuclear translocation assay; siRNA knockdown with alternative splicing readouts (RT-PCR)","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal binding assay, nuclear translocation assay, and loss-of-function splicing readout in single lab study","pmids":["28785060"],"is_preprint":false},{"year":2018,"finding":"ILDR2 plays a negligible role in hepatic steatosis; liver-specific and hepatocyte-specific Ildr2 knockout mice (congenital and acute Cre-mediated) do not develop hepatic steatosis, and the previously observed steatosis from shRNA was due to off-target effects on Dgka.","method":"Cre-mediated liver-specific Ildr2 knockout; shRNA rescue experiment in knockout background; RNA sequencing and BLAST alignment identifying Dgka as off-target","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — rigorous genetic knockout with multiple Cre strategies plus shRNA re-administration to knockouts definitively disproves prior shRNA-based hepatic steatosis claim; multiple orthogonal approaches","pmids":["29847571"],"is_preprint":false},{"year":2021,"finding":"ILDR2 interacts with ER-resident chaperones GRP78 and PDIA1 in pancreatic β-cells; GRP78 stabilizes ILDR2 by inhibiting ubiquitin-proteasome-mediated degradation. Adenoviral ILDR2 knockdown reduces glucose-responsive insulin secretion in MIN6 β-cells.","method":"TAP-tag purification of ILDR2-interacting proteins from MIN6 cells followed by mass spectrometry; co-immunoprecipitation validation; proteasome inhibitor assay; adenoviral shRNA knockdown with glucose-stimulated insulin secretion assay","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — TAP-tag MS plus Co-IP validation plus functional proteasome stabilization assay; single lab","pmids":["33863978"],"is_preprint":false},{"year":2024,"finding":"ILDR2 (angulin-3) is localized at tricellular junctions in primordial podocytes, then transiently moves to bicellular junctions during foot process interdigitation, and distributes in a sparse punctate pattern on adult podocyte foot processes. In podocyte injury models, angulin-3 shifts to bicellular localization between foot processes in a linear pattern.","method":"Monoclonal antibody-based superresolution and immunofluorescence microscopy in developmental stages, rodent injury models, and human nephrotic syndrome kidney biopsies","journal":"The American journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct localization experiments with newly established monoclonal antibody across multiple biological contexts; single lab, no functional consequence mechanistically resolved beyond localization change","pmids":["38311119"],"is_preprint":false},{"year":2024,"finding":"ILDR2 interacts with CLDN5 (claudin-5) in podocytes as shown by co-immunoprecipitation; Ildr2 knockout mice exhibit glomerular hypertrophy and decreased podocyte density, and LC-MS/MS proteomics of isolated glomeruli revealed increased matrix proteins (fibronectin, collagens), suggesting a protective role in glomerulopathies.","method":"Co-immunoprecipitation; Ildr2 knockout mouse phenotyping; LC-MS/MS proteomics of isolated glomeruli; scRNA-seq and superresolution microscopy","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP binding assay plus genetic knockout with defined cellular phenotype plus proteomic analysis; single lab, multiple orthogonal methods","pmids":["39640577"],"is_preprint":false},{"year":2024,"finding":"ILDR2 expressed on CD206hi macrophages in the sublingual mucosa promotes induction of Foxp3+ regulatory T cells from naïve CD4+ T cells in a TGF-β-dependent manner, contributing to antigen-specific immune tolerance.","method":"In vitro coculture of CD206hiILDR2+ macrophages with naïve CD4+ T cells; neutralizing anti-TGF-β antibody blockade; RNA-seq of sorted macrophage subpopulations","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vitro coculture functional assay with antibody blockade; single lab, receptor-level mechanism on macrophages not fully defined","pmids":["39626366"],"is_preprint":false}],"current_model":"ILDR2 is a type I transmembrane Ig-superfamily protein that functions as an 'angulin' family member at tricellular tight junctions where it recruits tricellulin; it resides in the ER membrane and is stabilized by GRP78 via protection from ubiquitin-proteasome degradation; it binds splicing factors TRA2A/TRA2B/SRSF1 and regulates alternative pre-mRNA splicing; it acts as a B7-like immune checkpoint that inhibits T cell responses and promotes Treg induction via TGF-β on macrophages; it interacts with CLDN5 in podocytes and its loss causes glomerular hypertrophy; and contrary to earlier shRNA-based reports, genetic knockout demonstrates ILDR2 plays a negligible direct role in hepatic steatosis."},"narrative":{"mechanistic_narrative":"ILDR2 is a type I transmembrane immunoglobulin-superfamily protein with context-dependent roles spanning tricellular junction organization, immune tolerance, and pre-mRNA splicing [PMID:23239027, PMID:29431694, PMID:28785060]. As an angulin family member alongside LSR and ILDR1, it localizes to tricellular contacts in epithelia and recruits tricellulin to tricellular tight junctions, although it confers only weak barrier function relative to its paralogs [PMID:23239027]. In the kidney, ILDR2 (angulin-3) marks tricellular and then bicellular junctions across podocyte development and injury, interacts with claudin-5 (CLDN5), and its genetic loss produces glomerular hypertrophy, reduced podocyte density, and accumulation of matrix proteins, consistent with a protective role in glomerulopathies [PMID:38311119, PMID:39640577]. Beyond junctions, ILDR2 acts as a negative regulator of T cell responses: an ILDR2 extracellular domain–Fc fusion binds a counterpart on activated T cells and suppresses proinflammatory cytokine production, and ILDR2 on CD206hi macrophages drives TGF-β-dependent induction of Foxp3+ regulatory T cells, supporting antigen-specific immune tolerance [PMID:29431694, PMID:39626366]. ILDR2 also binds the splicing factors TRA2A, TRA2B, and SRSF1, translocates to the nucleus in their presence, and regulates alternative splicing of TUBD1 and IQCB1 [PMID:28785060]. Rigorous liver- and hepatocyte-specific knockouts establish that ILDR2 plays a negligible direct role in hepatic steatosis, with earlier shRNA phenotypes attributable to off-target effects on Dgka [PMID:29847571].","teleology":[{"year":2012,"claim":"Established ILDR2 as an angulin-family tricellular junction protein, defining its first molecular role in epithelial junction architecture.","evidence":"Immunofluorescence localization and functional tricellulin recruitment assays in mouse epithelial tissues and cultured cells","pmids":["23239027"],"confidence":"High","gaps":["Weak barrier function relative to LSR/ILDR1 left its physiological junction role unclear","No structural basis for tricellulin recruitment defined"]},{"year":2013,"claim":"Localized ILDR2 to the ER membrane and linked hepatic ILDR2 manipulation to lipid homeostasis and ER stress, a claim later overturned at the gene level.","evidence":"Subcellular fractionation in cell lines plus adenoviral shRNA knockdown and overexpression in mouse liver with lipid and ER-stress readouts","pmids":["23826244"],"confidence":"Medium","gaps":["Causal primacy between lipid and ER-stress effects unresolved","Effects later attributed to shRNA off-target action on Dgka"]},{"year":2017,"claim":"Revealed a nuclear, RNA-regulatory function by showing ILDR2 binds splicing factors and controls alternative splicing, distinct from its junctional role.","evidence":"Co-IP/pulldown with TRA2A/TRA2B/SRSF1, nuclear translocation assay, and siRNA knockdown with RT-PCR splicing readouts","pmids":["28785060"],"confidence":"Medium","gaps":["Mechanism coupling a transmembrane protein to nuclear splicing unclear","Limited to two splicing targets in one lab"]},{"year":2018,"claim":"Defined ILDR2 as a B7-like negative immune regulator, identifying a new immunological function with therapeutic relevance.","evidence":"ILDR2-Fc binding assay on activated T cells, macrophage–T cell coculture cytokine assays, and collagen-induced arthritis model","pmids":["29431694"],"confidence":"Medium","gaps":["T cell counter-receptor identity undefined","Single lab"]},{"year":2018,"claim":"Disproved the prior hepatic steatosis model by genetic knockout, showing earlier shRNA phenotypes were off-target.","evidence":"Liver- and hepatocyte-specific Cre knockouts, shRNA rescue in knockout background, and RNA-seq/BLAST identifying Dgka as the off-target","pmids":["29847571"],"confidence":"High","gaps":["Does not address non-hepatic metabolic roles"]},{"year":2021,"claim":"Identified ER chaperone partners that stabilize ILDR2 and linked it to β-cell insulin secretion.","evidence":"TAP-tag MS, Co-IP validation of GRP78/PDIA1 interaction, proteasome inhibitor stabilization assay, and knockdown with glucose-stimulated insulin secretion in MIN6 cells","pmids":["33863978"],"confidence":"Medium","gaps":["Mechanism linking ILDR2 stability to insulin secretion undefined","Single lab"]},{"year":2024,"claim":"Extended the immune-tolerance role by showing macrophage ILDR2 drives Treg induction via TGF-β.","evidence":"Coculture of CD206hiILDR2+ macrophages with naïve CD4+ T cells, anti-TGF-β blockade, and RNA-seq of macrophage subsets","pmids":["39626366"],"confidence":"Medium","gaps":["Receptor-level mechanism on T cells not defined","In vitro only"]},{"year":2024,"claim":"Established a podocyte-protective junctional role through CLDN5 interaction and knockout glomerular phenotype.","evidence":"Co-IP with CLDN5, Ildr2 knockout phenotyping, glomerular LC-MS/MS proteomics, scRNA-seq, and superresolution imaging across development and injury","pmids":["38311119","39640577"],"confidence":"Medium","gaps":["Functional consequence of junctional relocalization in injury unresolved","Causal chain from CLDN5 binding to matrix accumulation not established"]},{"year":null,"claim":"How a single transmembrane protein integrates junctional, nuclear-splicing, ER-chaperone, and immune-checkpoint activities, and the identity of its T cell counter-receptor, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying mechanism connecting the distinct functional contexts","T cell receptor partner unidentified","No structural model"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[0,8]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[3,9]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,7]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[2,6]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,9]},{"term_id":"R-HSA-1500931","term_label":"Cell-Cell communication","supporting_discovery_ids":[0]}],"complexes":["tricellular tight junction"],"partners":["TRICELLULIN","TRA2A","TRA2B","SRSF1","HSPA5","PDIA1","CLDN5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q71H61","full_name":"Immunoglobulin-like domain-containing receptor 2","aliases":["Angulin-3"],"length_aa":639,"mass_kda":71.2,"function":"May be involved in ER stress pathways with effects on lipid homeostasis and insulin secretion. With ILDR1 and LSR, involved in the maintain of the epithelial barrier function through the recruitment of MARVELD2/tricellulin to tricellular tight junctions (By similarity). Also functions as a B7-like protein family member expressed on immune cells and inflamed tissue and with T-cell inhibitory activity (PubMed:29431694). In the inner ear, may regulate alternative pre-mRNA splicing via binding to TRA2A, TRA2B and SRSF1 (By similarity)","subcellular_location":"Endoplasmic reticulum membrane; Cell junction, tight junction; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q71H61/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ILDR2","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ILDR2","total_profiled":1310},"omim":[{"mim_id":"618111","title":"ZINC FINGER PROTEIN 64; ZFP64","url":"https://www.omim.org/entry/618111"},{"mim_id":"618081","title":"IMMUNOGLOBULIN-LIKE DOMAIN-CONTAINING RECEPTOR 2; ILDR2","url":"https://www.omim.org/entry/618081"},{"mim_id":"194544","title":"ZINC FINGER PROTEIN 70; ZNF70","url":"https://www.omim.org/entry/194544"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"brain","ntpm":6.0},{"tissue":"retina","ntpm":9.8},{"tissue":"testis","ntpm":8.2}],"url":"https://www.proteinatlas.org/search/ILDR2"},"hgnc":{"alias_symbol":[],"prev_symbol":["C1orf32"]},"alphafold":{"accession":"Q71H61","domains":[{"cath_id":"2.60.40.10","chopping":"19-58_99-168","consensus_level":"medium","plddt":91.5984,"start":19,"end":168},{"cath_id":"-","chopping":"61-94","consensus_level":"medium","plddt":63.6088,"start":61,"end":94},{"cath_id":"1.20.5","chopping":"181-214","consensus_level":"medium","plddt":77.1565,"start":181,"end":214}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q71H61","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q71H61-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q71H61-F1-predicted_aligned_error_v6.png","plddt_mean":56.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ILDR2","jax_strain_url":"https://www.jax.org/strain/search?query=ILDR2"},"sequence":{"accession":"Q71H61","fasta_url":"https://rest.uniprot.org/uniprotkb/Q71H61.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q71H61/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q71H61"}},"corpus_meta":[{"pmid":"23239027","id":"PMC_23239027","title":"Analysis of the 'angulin' proteins LSR, ILDR1 and ILDR2--tricellulin recruitment, epithelial barrier function and implication in deafness pathogenesis.","date":"2012","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/23239027","citation_count":175,"is_preprint":false},{"pmid":"29431694","id":"PMC_29431694","title":"ILDR2 Is a Novel B7-like Protein That Negatively Regulates T Cell Responses.","date":"2018","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/29431694","citation_count":27,"is_preprint":false},{"pmid":"23826244","id":"PMC_23826244","title":"ILDR2: an endoplasmic reticulum resident molecule mediating hepatic lipid homeostasis.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23826244","citation_count":20,"is_preprint":false},{"pmid":"29431690","id":"PMC_29431690","title":"ILDR2-Fc Is a Novel Regulator of Immune Homeostasis and Inducer of Antigen-Specific Immune Tolerance.","date":"2018","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/29431690","citation_count":18,"is_preprint":false},{"pmid":"28785060","id":"PMC_28785060","title":"Angulin proteins ILDR1 and ILDR2 regulate alternative pre-mRNA splicing through binding to splicing factors TRA2A, TRA2B, or SRSF1.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28785060","citation_count":17,"is_preprint":false},{"pmid":"32312711","id":"PMC_32312711","title":"Characterization of BAY 1905254, an Immune Checkpoint Inhibitor Targeting the Immunoglobulin-Like Domain Containing Receptor 2 (ILDR2).","date":"2020","source":"Cancer immunology research","url":"https://pubmed.ncbi.nlm.nih.gov/32312711","citation_count":8,"is_preprint":false},{"pmid":"39640577","id":"PMC_39640577","title":"The role of the tricellular junction protein ILDR2 in glomerulopathies: Expression patterns and functional insights.","date":"2024","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/39640577","citation_count":3,"is_preprint":false},{"pmid":"33863978","id":"PMC_33863978","title":"ILDR2 stabilization is regulated by its interaction with GRP78.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33863978","citation_count":3,"is_preprint":false},{"pmid":"29847571","id":"PMC_29847571","title":"ILDR2 has a negligible role in hepatic steatosis.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29847571","citation_count":2,"is_preprint":false},{"pmid":"38311119","id":"PMC_38311119","title":"Bicellular Localization of Tricellular Junctional Protein Angulin-3/ILDR2 Allows Detection of Podocyte Injury.","date":"2024","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/38311119","citation_count":1,"is_preprint":false},{"pmid":"39626366","id":"PMC_39626366","title":"Sublingual macrophage-associated ILDR2 contributes to immune tolerance via Treg induction.","date":"2024","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/39626366","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7670,"output_tokens":2565,"usd":0.030742,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9833,"output_tokens":2867,"usd":0.06042,"stage2_stop_reason":"end_turn"},"total_usd":0.091162,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"ILDR2 localizes at tricellular contacts (TCs) in epithelial tissues and recruits tricellulin to tricellular tight junctions (tTJs), functioning as an 'angulin' family protein alongside LSR and ILDR1.\",\n      \"method\": \"Immunofluorescence localization in mouse epithelial tissues and cultured epithelial cells; functional tricellulin recruitment assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional consequence (tricellulin recruitment), multiple epithelial cell types and tissues examined, consistent with broader angulin family framework\",\n      \"pmids\": [\"23239027\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"ILDR2 provides a much weaker epithelial barrier function compared to LSR and ILDR1 when introduced into cultured epithelial cells.\",\n      \"method\": \"Introduction of ILDR2 into cultured epithelial cells followed by barrier function assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, single functional assay in cultured cells showing weaker barrier relative to LSR/ILDR1\",\n      \"pmids\": [\"23239027\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"ILDR2 is primarily located in the endoplasmic reticulum membrane in hepatoma and neuronal cells, and manipulation of hepatic ILDR2 expression (knockdown or overexpression via adenovirus) affects hepatic lipid homeostasis and ER stress pathway gene expression.\",\n      \"method\": \"Subcellular fractionation/ER localization in cell lines; adenoviral shRNA knockdown and CMV-driven overexpression in mouse liver; measurement of hepatic triglycerides, cholesterol, VLDL, and ER stress gene expression\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct ER localization plus gain- and loss-of-function in vivo with lipid and ER stress readouts; however, causal primacy between lipid effects and ER stress effects not resolved in this study\",\n      \"pmids\": [\"23826244\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ILDR2 negatively regulates T cell responses; an ILDR2 extracellular domain–Fc fusion protein binds to a putative counterpart on activated T cells and inhibits proinflammatory cytokine/chemokine production in autologous macrophage–T cell cocultures, and shows benefit in the collagen-induced arthritis model.\",\n      \"method\": \"ILDR2-Fc fusion protein binding assay on activated T cells; in vitro coculture cytokine inhibition assay; collagen-induced arthritis mouse model\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — binding assay plus in vitro functional assay plus in vivo disease model; single lab, receptor identity on T cells not yet fully defined\",\n      \"pmids\": [\"29431694\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ILDR2 binds to splicing factors TRA2A, TRA2B, and SRSF1, translocates into the nucleus when these splicing factors are present, and regulates alternative pre-mRNA splicing of TUBD1 and IQCB1; siRNA knockdown of endogenous ILDR2 in cultured cells affects alternative splicing of these targets.\",\n      \"method\": \"Co-immunoprecipitation/pulldown with splicing factors; nuclear translocation assay; siRNA knockdown with alternative splicing readouts (RT-PCR)\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding assay, nuclear translocation assay, and loss-of-function splicing readout in single lab study\",\n      \"pmids\": [\"28785060\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ILDR2 plays a negligible role in hepatic steatosis; liver-specific and hepatocyte-specific Ildr2 knockout mice (congenital and acute Cre-mediated) do not develop hepatic steatosis, and the previously observed steatosis from shRNA was due to off-target effects on Dgka.\",\n      \"method\": \"Cre-mediated liver-specific Ildr2 knockout; shRNA rescue experiment in knockout background; RNA sequencing and BLAST alignment identifying Dgka as off-target\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — rigorous genetic knockout with multiple Cre strategies plus shRNA re-administration to knockouts definitively disproves prior shRNA-based hepatic steatosis claim; multiple orthogonal approaches\",\n      \"pmids\": [\"29847571\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ILDR2 interacts with ER-resident chaperones GRP78 and PDIA1 in pancreatic β-cells; GRP78 stabilizes ILDR2 by inhibiting ubiquitin-proteasome-mediated degradation. Adenoviral ILDR2 knockdown reduces glucose-responsive insulin secretion in MIN6 β-cells.\",\n      \"method\": \"TAP-tag purification of ILDR2-interacting proteins from MIN6 cells followed by mass spectrometry; co-immunoprecipitation validation; proteasome inhibitor assay; adenoviral shRNA knockdown with glucose-stimulated insulin secretion assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — TAP-tag MS plus Co-IP validation plus functional proteasome stabilization assay; single lab\",\n      \"pmids\": [\"33863978\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ILDR2 (angulin-3) is localized at tricellular junctions in primordial podocytes, then transiently moves to bicellular junctions during foot process interdigitation, and distributes in a sparse punctate pattern on adult podocyte foot processes. In podocyte injury models, angulin-3 shifts to bicellular localization between foot processes in a linear pattern.\",\n      \"method\": \"Monoclonal antibody-based superresolution and immunofluorescence microscopy in developmental stages, rodent injury models, and human nephrotic syndrome kidney biopsies\",\n      \"journal\": \"The American journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct localization experiments with newly established monoclonal antibody across multiple biological contexts; single lab, no functional consequence mechanistically resolved beyond localization change\",\n      \"pmids\": [\"38311119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ILDR2 interacts with CLDN5 (claudin-5) in podocytes as shown by co-immunoprecipitation; Ildr2 knockout mice exhibit glomerular hypertrophy and decreased podocyte density, and LC-MS/MS proteomics of isolated glomeruli revealed increased matrix proteins (fibronectin, collagens), suggesting a protective role in glomerulopathies.\",\n      \"method\": \"Co-immunoprecipitation; Ildr2 knockout mouse phenotyping; LC-MS/MS proteomics of isolated glomeruli; scRNA-seq and superresolution microscopy\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP binding assay plus genetic knockout with defined cellular phenotype plus proteomic analysis; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"39640577\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ILDR2 expressed on CD206hi macrophages in the sublingual mucosa promotes induction of Foxp3+ regulatory T cells from naïve CD4+ T cells in a TGF-β-dependent manner, contributing to antigen-specific immune tolerance.\",\n      \"method\": \"In vitro coculture of CD206hiILDR2+ macrophages with naïve CD4+ T cells; neutralizing anti-TGF-β antibody blockade; RNA-seq of sorted macrophage subpopulations\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vitro coculture functional assay with antibody blockade; single lab, receptor-level mechanism on macrophages not fully defined\",\n      \"pmids\": [\"39626366\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ILDR2 is a type I transmembrane Ig-superfamily protein that functions as an 'angulin' family member at tricellular tight junctions where it recruits tricellulin; it resides in the ER membrane and is stabilized by GRP78 via protection from ubiquitin-proteasome degradation; it binds splicing factors TRA2A/TRA2B/SRSF1 and regulates alternative pre-mRNA splicing; it acts as a B7-like immune checkpoint that inhibits T cell responses and promotes Treg induction via TGF-β on macrophages; it interacts with CLDN5 in podocytes and its loss causes glomerular hypertrophy; and contrary to earlier shRNA-based reports, genetic knockout demonstrates ILDR2 plays a negligible direct role in hepatic steatosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ILDR2 is a type I transmembrane immunoglobulin-superfamily protein with context-dependent roles spanning tricellular junction organization, immune tolerance, and pre-mRNA splicing [#0, #3, #4]. As an angulin family member alongside LSR and ILDR1, it localizes to tricellular contacts in epithelia and recruits tricellulin to tricellular tight junctions, although it confers only weak barrier function relative to its paralogs [#0, #1]. In the kidney, ILDR2 (angulin-3) marks tricellular and then bicellular junctions across podocyte development and injury, interacts with claudin-5 (CLDN5), and its genetic loss produces glomerular hypertrophy, reduced podocyte density, and accumulation of matrix proteins, consistent with a protective role in glomerulopathies [#7, #8]. Beyond junctions, ILDR2 acts as a negative regulator of T cell responses: an ILDR2 extracellular domain–Fc fusion binds a counterpart on activated T cells and suppresses proinflammatory cytokine production, and ILDR2 on CD206hi macrophages drives TGF-β-dependent induction of Foxp3+ regulatory T cells, supporting antigen-specific immune tolerance [#3, #9]. ILDR2 also binds the splicing factors TRA2A, TRA2B, and SRSF1, translocates to the nucleus in their presence, and regulates alternative splicing of TUBD1 and IQCB1 [#4]. Rigorous liver- and hepatocyte-specific knockouts establish that ILDR2 plays a negligible direct role in hepatic steatosis, with earlier shRNA phenotypes attributable to off-target effects on Dgka [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established ILDR2 as an angulin-family tricellular junction protein, defining its first molecular role in epithelial junction architecture.\",\n      \"evidence\": \"Immunofluorescence localization and functional tricellulin recruitment assays in mouse epithelial tissues and cultured cells\",\n      \"pmids\": [\"23239027\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Weak barrier function relative to LSR/ILDR1 left its physiological junction role unclear\", \"No structural basis for tricellulin recruitment defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Localized ILDR2 to the ER membrane and linked hepatic ILDR2 manipulation to lipid homeostasis and ER stress, a claim later overturned at the gene level.\",\n      \"evidence\": \"Subcellular fractionation in cell lines plus adenoviral shRNA knockdown and overexpression in mouse liver with lipid and ER-stress readouts\",\n      \"pmids\": [\"23826244\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal primacy between lipid and ER-stress effects unresolved\", \"Effects later attributed to shRNA off-target action on Dgka\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealed a nuclear, RNA-regulatory function by showing ILDR2 binds splicing factors and controls alternative splicing, distinct from its junctional role.\",\n      \"evidence\": \"Co-IP/pulldown with TRA2A/TRA2B/SRSF1, nuclear translocation assay, and siRNA knockdown with RT-PCR splicing readouts\",\n      \"pmids\": [\"28785060\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism coupling a transmembrane protein to nuclear splicing unclear\", \"Limited to two splicing targets in one lab\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined ILDR2 as a B7-like negative immune regulator, identifying a new immunological function with therapeutic relevance.\",\n      \"evidence\": \"ILDR2-Fc binding assay on activated T cells, macrophage–T cell coculture cytokine assays, and collagen-induced arthritis model\",\n      \"pmids\": [\"29431694\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"T cell counter-receptor identity undefined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Disproved the prior hepatic steatosis model by genetic knockout, showing earlier shRNA phenotypes were off-target.\",\n      \"evidence\": \"Liver- and hepatocyte-specific Cre knockouts, shRNA rescue in knockout background, and RNA-seq/BLAST identifying Dgka as the off-target\",\n      \"pmids\": [\"29847571\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address non-hepatic metabolic roles\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified ER chaperone partners that stabilize ILDR2 and linked it to β-cell insulin secretion.\",\n      \"evidence\": \"TAP-tag MS, Co-IP validation of GRP78/PDIA1 interaction, proteasome inhibitor stabilization assay, and knockdown with glucose-stimulated insulin secretion in MIN6 cells\",\n      \"pmids\": [\"33863978\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking ILDR2 stability to insulin secretion undefined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the immune-tolerance role by showing macrophage ILDR2 drives Treg induction via TGF-β.\",\n      \"evidence\": \"Coculture of CD206hiILDR2+ macrophages with naïve CD4+ T cells, anti-TGF-β blockade, and RNA-seq of macrophage subsets\",\n      \"pmids\": [\"39626366\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Receptor-level mechanism on T cells not defined\", \"In vitro only\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established a podocyte-protective junctional role through CLDN5 interaction and knockout glomerular phenotype.\",\n      \"evidence\": \"Co-IP with CLDN5, Ildr2 knockout phenotyping, glomerular LC-MS/MS proteomics, scRNA-seq, and superresolution imaging across development and injury\",\n      \"pmids\": [\"38311119\", \"39640577\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of junctional relocalization in injury unresolved\", \"Causal chain from CLDN5 binding to matrix accumulation not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single transmembrane protein integrates junctional, nuclear-splicing, ER-chaperone, and immune-checkpoint activities, and the identity of its T cell counter-receptor, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying mechanism connecting the distinct functional contexts\", \"T cell receptor partner unidentified\", \"No structural model\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [3, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 9]},\n      {\"term_id\": \"R-HSA-1500931\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"tricellular tight junction\"],\n    \"partners\": [\"TRICELLULIN\", \"TRA2A\", \"TRA2B\", \"SRSF1\", \"HSPA5\", \"PDIA1\", \"CLDN5\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}