{"gene":"KIRREL2","run_date":"2026-06-10T02:59:49","timeline":{"discoveries":[{"year":2003,"finding":"KIRREL2 (filtrin) is a type I transmembrane protein with five Ig domains, one transmembrane domain, and an intracellular domain, belonging to the immunoglobulin superfamily with structural homology to nephrin, NEPH1, and Drosophila RST. Expression is predominantly in pancreatic beta cells and also in the nervous system.","method":"Computational gene discovery, RT-PCR, Northern blot, immunohistochemistry","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multiple orthogonal methods (computational, RT-PCR, Northern blot, IHC) from a single lab establishing basic structural identity and expression pattern","pmids":["12837264"],"is_preprint":false},{"year":2003,"finding":"Filtrin (KIRREL2/NEPH3) is expressed in kidney glomeruli and localizes to the slit diaphragm region, and immunoblotting detects a specific band at ~107 kDa in human and rat glomeruli, consistent with its proposed role as a component of the glomerular filtration barrier.","method":"RT-PCR, immunoblotting, immunofluorescence microscopy","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multiple orthogonal methods (RT-PCR, Western blot, immunofluorescence) in a single lab establishing localization","pmids":["12504092"],"is_preprint":false},{"year":2007,"finding":"Filtrin (KIRREL2/NEPH3) localizes to the slit diaphragm of podocyte foot processes by immunoelectron microscopy, and its mRNA and protein expression are down-regulated in human proteinuric glomerular diseases including focal segmental glomerulosclerosis.","method":"Quantitative RT-PCR, immunofluorescence microscopy, immunoelectron microscopy","journal":"Nephrology, dialysis, transplantation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — immunoelectron microscopy directly localizes protein to slit diaphragm; multiple orthogonal methods in single lab","pmids":["17442742"],"is_preprint":false},{"year":2009,"finding":"Ptf1a transcription factor directly controls expression of Neph3 (KIRREL2) by binding to a PTF-binding motif in the 5'-flanking region of the Neph3 gene and activating transcription; Neph3 expression is lost in Ptf1a-null mice and induced by ectopic Ptf1a expression. Additionally, Neph3 interacts homophilically and heterophilically with Nephrin.","method":"ChIP, promoter reporter assay, in vivo Ptf1a knockout mice, ectopic Ptf1a expression, co-immunoprecipitation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (ChIP, reporter assay, KO mice, ectopic expression, co-IP) establishing direct transcriptional regulation and protein-protein interaction","pmids":["19887377"],"is_preprint":false},{"year":2009,"finding":"Neph3 (KIRREL2) is a direct downstream target gene of Ptf1a in cerebellar GABAergic progenitors, marking the ventricular zone progenitors that give rise to Purkinje cells. Neph3+ E-cadherin-high cells are PC progenitors while Neph3+ E-cadherin-low cells are interneuron progenitors.","method":"FACS sorting, in vitro cell fate assay, in vivo lineage tracing with Neph3 promoter-driven GFP transgenic mice, short-term in vivo tracing","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (FACS, in vitro fate mapping, in vivo lineage tracing) from a single lab robustly establishing Neph3 as a cell-fate marker and direct Ptf1a target in cerebellum","pmids":["20004188"],"is_preprint":false},{"year":2009,"finding":"NF-κB and Sp1 transcription factors are key regulators of basal Neph3 (KIRREL2) expression in podocytes: they bind to response elements in the proximal Neph3 promoter (-105 to -57), are essential for basal transcriptional activity by mutational screening, and overexpression of NF-κB increases endogenous Neph3 gene expression.","method":"Promoter reporter gene constructs, site-directed mutagenesis, co-transfection, chromatin immunoprecipitation in cultured human podocytes","journal":"BMC molecular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (reporter assay, mutagenesis, ChIP, co-transfection with endogenous read-out) in a single lab","pmids":["19703278"],"is_preprint":false},{"year":2011,"finding":"Neph3 (KIRREL2) homodimerizes and heterodimerizes with nephrin and Neph1. Neph3 alone can induce cell adhesion in L fibroblasts that lack endogenous adhesion activity. Nephrin requires trans-interaction with Neph1 or Neph3 to promote cell-cell contact formation. Trans-interaction of nephrin with Neph3 leads to down-regulation of nephrin tyrosine phosphorylation.","method":"Co-immunoprecipitation, L fibroblast cell adhesion assay, tyrosine phosphorylation analysis","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — co-IP establishing dimerization partners, functional cell adhesion assay in heterologous system, phosphorylation readout; multiple orthogonal methods in single lab","pmids":["21306299"],"is_preprint":false},{"year":2011,"finding":"WT1 and NF-κB synergistically activate the Neph3 (KIRREL2) gene promoter in podocytes; WT1 and NF-κB physically interact with each other, and TNF-α increases Neph3 mRNA expression via NF-κB. DNA methylation silences Neph3 expression in a cell-type and differentiation stage-dependent manner.","method":"Reporter gene assay, chromatin immunoprecipitation, co-immunoprecipitation, overexpression studies, TNF-α treatment with pathway inhibitor, 5-aza-2'-deoxycytidine demethylation treatment, quantitative PCR","journal":"Nephrology, dialysis, transplantation","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (ChIP, Co-IP, reporter assay, pharmacological treatments with quantitative readouts) in a single lab","pmids":["21980157"],"is_preprint":false},{"year":2011,"finding":"Morpholino knockdown of neph3 in zebrafish results in altered glomerular morphology, dilated pronephric tubules, pericardial edema, distorted body curvature, and aberrant brain morphology; the pericardial edema/body curvature phenotype is rescued by wild-type neph3 mRNA, establishing a direct functional role for Neph3 in glomerular and neural development.","method":"Antisense morpholino oligonucleotide knockdown in zebrafish, histology, mRNA rescue experiment","journal":"Differentiation; research in biological diversity","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — morpholino loss-of-function with mRNA rescue in zebrafish, single lab","pmids":["22099175"],"is_preprint":false},{"year":2017,"finding":"The NEPH3 variant V353M (KIRREL2) disrupts Neph3 homodimerization and Neph3-Nephrin heterodimerization and is associated with differential activation of the unfolded protein response pathway when overexpressed in stressed podocyte cells, indicating that this variant impairs normal protein-protein interactions and protein folding.","method":"Functional dimerization assay, unfolded protein response pathway assay in cultured podocyte cells, genetic association study","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional dimerization and UPR assays in cell culture with a disease variant, single lab","pmids":["28334007"],"is_preprint":false},{"year":2019,"finding":"Kirrel2 is required for axonal coalescence of MOR174-9- and M72-expressing olfactory sensory neurons (OSNs) projecting to the DII region of the olfactory bulb; loss of Kirrel2 causes these OSN axons to target ectopic glomeruli. Kirrel2 and Kirrel3 are dispensable for OSN axon coalescence in the most dorsal (DI) region, indicating region-specific requirements.","method":"Kirrel2 knockout mice (loss-of-function), double Kirrel2/Kirrel3 knockout, examination of axonal projections of specific OSN populations","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic KO with defined cellular phenotype (ectopic glomeruli), double KO for epistasis, multiple OSN populations examined","pmids":["31142543"],"is_preprint":false},{"year":2006,"finding":"Filtrin (KIRREL2/NEPH3) is expressed at the gene and protein level in Langerhans islets of the pancreas, co-localizing with beta cell markers, establishing its presence in a second epithelial structure (pancreatic islets) analogous to its podocyte slit diaphragm expression.","method":"RT-PCR, immunoblotting, immunofluorescence","journal":"Molecular and cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multiple orthogonal localization methods (RT-PCR, Western, IF) in single lab establishing expression/localization in pancreatic islets","pmids":["16841182"],"is_preprint":false}],"current_model":"KIRREL2 (NEPH3/filtrin) is an immunoglobulin superfamily transmembrane cell adhesion molecule that localizes to the slit diaphragm of kidney podocytes and is transcriptionally regulated by Ptf1a, NF-κB, Sp1, WT1, and DNA methylation; it forms homo- and heterodimers with nephrin and Neph1, promotes cell-cell adhesion in trans, and down-regulates nephrin tyrosine phosphorylation upon contact formation; in the nervous system, it is a direct Ptf1a target marking cerebellar GABAergic progenitors and is required for proper olfactory sensory neuron axon coalescence into glomeruli in the DII region of the olfactory bulb."},"narrative":{"mechanistic_narrative":"KIRREL2 (NEPH3/filtrin) is an immunoglobulin-superfamily type I transmembrane cell-adhesion molecule with five extracellular Ig domains that functions at specialized cell-cell junctions in epithelia and in neural circuit assembly [PMID:12837264]. In the kidney it localizes to the slit diaphragm of podocyte foot processes, where it engages in homophilic and heterophilic trans-interactions with nephrin and Neph1 to mediate cell-cell adhesion, and its trans-engagement with nephrin down-regulates nephrin tyrosine phosphorylation, linking contact formation to signaling at the filtration barrier [PMID:17442742, PMID:19887377, PMID:21306299]. Its expression is controlled by a convergent transcriptional program: Ptf1a binds the 5'-flanking region to directly activate transcription, NF-κB and Sp1 drive basal promoter activity, WT1 synergizes with NF-κB, and DNA methylation silences the gene in a stage- and cell-type-dependent manner [PMID:19887377, PMID:19703278, PMID:21980157]. Beyond the kidney, KIRREL2 is a direct Ptf1a target that marks cerebellar GABAergic ventricular-zone progenitors and is required for region-specific coalescence of olfactory sensory neuron axons into glomeruli in the DII domain of the olfactory bulb, with loss of function producing ectopic glomerular targeting [PMID:20004188, PMID:31142543]. A V353M variant that disrupts both homo- and heterodimerization and perturbs the unfolded protein response connects its adhesive function to podocyte disease [PMID:28334007].","teleology":[{"year":2003,"claim":"Establishing the molecular identity of KIRREL2 was the first step: it was unknown what kind of protein it was, and structural characterization placed it as a nephrin/NEPH1-related Ig-superfamily adhesion molecule expressed in pancreatic beta cells and nervous system.","evidence":"Computational gene discovery with RT-PCR, Northern blot and immunohistochemistry","pmids":["12837264"],"confidence":"Medium","gaps":["Did not establish binding partners or function","Tissue expression survey only, no mechanism"]},{"year":2003,"claim":"Localizing the protein answered where it acts: immunolocalization placed filtrin at the glomerular slit diaphragm, implicating it as a component of the filtration barrier.","evidence":"RT-PCR, immunoblotting and immunofluorescence in human and rat glomeruli","pmids":["12504092"],"confidence":"Medium","gaps":["Light-level localization only; ultrastructural placement not yet shown","Functional contribution to filtration untested"]},{"year":2006,"claim":"Whether KIRREL2 acts only at the slit diaphragm was addressed by showing it is also expressed in pancreatic islet beta cells, extending its association to a second specialized epithelial structure.","evidence":"RT-PCR, immunoblotting and immunofluorescence in pancreatic Langerhans islets","pmids":["16841182"],"confidence":"Medium","gaps":["Functional role in islets not determined","No partner or signaling data in beta cells"]},{"year":2007,"claim":"Ultrastructural localization and disease correlation refined the role: immunoelectron microscopy confirmed slit-diaphragm placement and showed down-regulation in human proteinuric disease, linking KIRREL2 to barrier integrity.","evidence":"Quantitative RT-PCR, immunofluorescence and immunoelectron microscopy in normal and FSGS human glomeruli","pmids":["17442742"],"confidence":"Medium","gaps":["Correlation not causation in human disease","Mechanism of down-regulation unknown"]},{"year":2009,"claim":"How KIRREL2 expression is controlled and what it binds were answered together: Ptf1a directly activates the gene via a promoter motif, and KIRREL2 interacts homo- and heterophilically with nephrin, establishing both an upstream regulator and a physical adhesion partner.","evidence":"ChIP, promoter reporter assays, Ptf1a-null mice, ectopic expression, and co-immunoprecipitation","pmids":["19887377"],"confidence":"High","gaps":["Functional consequence of nephrin interaction not yet defined","Other transcriptional inputs not assessed"]},{"year":2009,"claim":"The neural role was identified: lineage tracing showed KIRREL2 is a direct Ptf1a target marking cerebellar GABAergic ventricular-zone progenitors, distinguishing Purkinje cell from interneuron progenitor pools by E-cadherin level.","evidence":"FACS, in vitro fate assays and in vivo lineage tracing with Neph3 promoter-GFP transgenic mice","pmids":["20004188"],"confidence":"High","gaps":["KIRREL2 used as marker; its functional requirement in cerebellar fate not tested","Adhesive mechanism in progenitors unaddressed"]},{"year":2009,"claim":"The basal transcriptional machinery was defined: NF-κB and Sp1 bind the proximal promoter and are essential for basal activity in podocytes, identifying the core regulators of constitutive expression.","evidence":"Promoter reporter constructs, site-directed mutagenesis, ChIP and co-transfection in cultured human podocytes","pmids":["19703278"],"confidence":"High","gaps":["Signal inputs controlling these factors not defined","Cell-type specificity of regulation not explained"]},{"year":2011,"claim":"The mechanistic role of the interactions was established: KIRREL2 homo- and heterodimerizes with nephrin and Neph1, can drive adhesion autonomously in fibroblasts, and its trans-engagement of nephrin down-regulates nephrin tyrosine phosphorylation, coupling adhesion to signaling.","evidence":"Co-immunoprecipitation, L fibroblast adhesion assay and tyrosine phosphorylation analysis","pmids":["21306299"],"confidence":"High","gaps":["Phosphatase/kinase mediating dephosphorylation not identified","In vivo relevance of phosphorylation control not demonstrated"]},{"year":2011,"claim":"Transcriptional control was integrated: WT1 synergizes with NF-κB, TNF-α induces expression via NF-κB, and DNA methylation silences the gene, showing combinatorial and epigenetic regulation.","evidence":"Reporter assays, ChIP, co-IP, TNF-α treatment with pathway inhibitor, and 5-aza-2'-deoxycytidine demethylation with qPCR","pmids":["21980157"],"confidence":"High","gaps":["Physiological trigger for methylation changes not defined","Interplay with Ptf1a not reconciled"]},{"year":2011,"claim":"In vivo requirement was tested: morpholino knockdown of neph3 in zebrafish produced glomerular and neural defects rescued by wild-type mRNA, providing loss-of-function evidence for a developmental role.","evidence":"Antisense morpholino knockdown in zebrafish with histology and mRNA rescue","pmids":["22099175"],"confidence":"Medium","gaps":["Morpholino specificity caveats","Cellular mechanism behind phenotypes not resolved"]},{"year":2017,"claim":"A disease-linked variant connected dimerization to pathology: V353M disrupts homo- and heterodimerization and alters the unfolded protein response, mechanistically linking impaired KIRREL2 interactions to podocyte dysfunction.","evidence":"Functional dimerization and UPR assays in cultured podocytes with genetic association","pmids":["28334007"],"confidence":"Medium","gaps":["Causality in patient kidney disease not established","Single variant in cell-culture overexpression"]},{"year":2019,"claim":"A definitive in vivo neural function was shown: Kirrel2 knockout mice display ectopic glomerular targeting of specific olfactory sensory neuron populations in the DII region, establishing a region-specific role in axon coalescence.","evidence":"Kirrel2 single and Kirrel2/Kirrel3 double knockout mice with analysis of defined OSN axon projections","pmids":["31142543"],"confidence":"High","gaps":["Molecular partners of KIRREL2 in OSN axons not identified","Mechanism of regional specificity unexplained"]},{"year":null,"claim":"It remains unknown how KIRREL2's adhesion and signaling functions are mechanistically deployed across its different tissues, including its functional role in pancreatic beta cells and the downstream effectors linking trans-adhesion to nephrin dephosphorylation in vivo.","evidence":"","pmids":[],"confidence":"Low","gaps":["No identified phosphatase mediating nephrin dephosphorylation","Beta-cell function uncharacterized","Cytoplasmic effectors of KIRREL2 signaling not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[3,6]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1,2]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4,10]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[3,5,7]}],"complexes":["slit diaphragm"],"partners":["NPHS1","KIRREL1","PTF1A","WT1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6UWL6","full_name":"Kin of IRRE-like protein 2","aliases":["Kin of irregular chiasm-like protein 2","Nephrin-like protein 3"],"length_aa":708,"mass_kda":75.1,"function":"May regulate basal insulin secretion","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q6UWL6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/KIRREL2","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/KIRREL2","total_profiled":1310},"omim":[{"mim_id":"607762","title":"KIRRE-LIKE NEPHRIN FAMILY ADHESION MOLECULE 2; KIRREL2","url":"https://www.omim.org/entry/607762"},{"mim_id":"607761","title":"KIRRE-LIKE NEPHRIN FAMILY ADHESION MOLECULE 3; KIRREL3","url":"https://www.omim.org/entry/607761"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Centriolar satellite","reliability":"Supported"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"pancreas","ntpm":67.0}],"url":"https://www.proteinatlas.org/search/KIRREL2"},"hgnc":{"alias_symbol":["NLG1","NEPH3","FILTRIN","DKFZp564A1164","MGC15718"],"prev_symbol":[]},"alphafold":{"accession":"Q6UWL6","domains":[{"cath_id":"2.60.40.10","chopping":"26-121","consensus_level":"high","plddt":93.3712,"start":26,"end":121},{"cath_id":"2.60.40.10","chopping":"124-306","consensus_level":"medium","plddt":88.9568,"start":124,"end":306},{"cath_id":"2.60.40.10","chopping":"312-396","consensus_level":"high","plddt":89.6621,"start":312,"end":396},{"cath_id":"2.60.40.10","chopping":"406-505","consensus_level":"high","plddt":85.5068,"start":406,"end":505}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6UWL6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6UWL6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6UWL6-F1-predicted_aligned_error_v6.png","plddt_mean":75.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=KIRREL2","jax_strain_url":"https://www.jax.org/strain/search?query=KIRREL2"},"sequence":{"accession":"Q6UWL6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6UWL6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6UWL6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6UWL6"}},"corpus_meta":[{"pmid":"20004188","id":"PMC_20004188","title":"Purkinje cells originate from cerebellar ventricular zone progenitors positive for Neph3 and E-cadherin.","date":"2009","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/20004188","citation_count":57,"is_preprint":false},{"pmid":"12504092","id":"PMC_12504092","title":"Filtrin is a novel member of nephrin-like proteins.","date":"2003","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/12504092","citation_count":44,"is_preprint":false},{"pmid":"12837264","id":"PMC_12837264","title":"Kirrel2, a novel immunoglobulin superfamily gene expressed primarily in beta cells of the pancreatic islets.","date":"2003","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/12837264","citation_count":28,"is_preprint":false},{"pmid":"24219158","id":"PMC_24219158","title":"Functions of the podocyte proteins nephrin and Neph3 and the transcriptional regulation of their genes.","date":"2014","source":"Clinical science (London, England : 1979)","url":"https://pubmed.ncbi.nlm.nih.gov/24219158","citation_count":27,"is_preprint":false},{"pmid":"19887377","id":"PMC_19887377","title":"Ptf1a directly controls expression of immunoglobulin superfamily molecules Nephrin and Neph3 in the developing central nervous system.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19887377","citation_count":25,"is_preprint":false},{"pmid":"21306299","id":"PMC_21306299","title":"Trans-interaction of nephrin and Neph1/Neph3 induces cell adhesion that associates with decreased tyrosine phosphorylation of nephrin.","date":"2011","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/21306299","citation_count":23,"is_preprint":false},{"pmid":"21980157","id":"PMC_21980157","title":"Transcription of nephrin-Neph3 gene pair is synergistically activated by WT1 and NF-κB and silenced by DNA methylation.","date":"2011","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association","url":"https://pubmed.ncbi.nlm.nih.gov/21980157","citation_count":21,"is_preprint":false},{"pmid":"28334007","id":"PMC_28334007","title":"A functional variant in NEPH3 gene confers high risk of renal failure in primary hematuric glomerulopathies. Evidence for predisposition to microalbuminuria in the general population.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28334007","citation_count":20,"is_preprint":false},{"pmid":"31142543","id":"PMC_31142543","title":"Kirrel2 is differentially required in populations of olfactory sensory neurons for the targeting of axons in the olfactory bulb.","date":"2019","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/31142543","citation_count":17,"is_preprint":false},{"pmid":"23325127","id":"PMC_23325127","title":"Glomerulopathy and mutations in NPHS1 and KIRREL2 in soft-coated Wheaten Terrier dogs.","date":"2013","source":"Mammalian genome : official journal of the International Mammalian Genome Society","url":"https://pubmed.ncbi.nlm.nih.gov/23325127","citation_count":16,"is_preprint":false},{"pmid":"17442742","id":"PMC_17442742","title":"Expression of filtrin in human glomerular diseases.","date":"2007","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association","url":"https://pubmed.ncbi.nlm.nih.gov/17442742","citation_count":15,"is_preprint":false},{"pmid":"19703278","id":"PMC_19703278","title":"Regulation of Neph3 gene in podocytes--key roles of transcription factors NF-kappaB and Sp1.","date":"2009","source":"BMC molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/19703278","citation_count":14,"is_preprint":false},{"pmid":"16841182","id":"PMC_16841182","title":"Podocyte-associated proteins FAT, alpha-actinin-4 and filtrin are expressed in Langerhans islets of the pancreas.","date":"2006","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16841182","citation_count":13,"is_preprint":false},{"pmid":"22099175","id":"PMC_22099175","title":"Neph3 associates with regulation of glomerular and neural development in zebrafish.","date":"2011","source":"Differentiation; research in biological diversity","url":"https://pubmed.ncbi.nlm.nih.gov/22099175","citation_count":10,"is_preprint":false},{"pmid":"16741999","id":"PMC_16741999","title":"Densin and filtrin in the pancreas and in the kidney, targets for humoral autoimmunity in patients with type 1 diabetes.","date":"2007","source":"Diabetes/metabolism research and reviews","url":"https://pubmed.ncbi.nlm.nih.gov/16741999","citation_count":6,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10057,"output_tokens":3111,"usd":0.038418,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10490,"output_tokens":3747,"usd":0.073063,"stage2_stop_reason":"end_turn"},"total_usd":0.111481,"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\": 2003,\n      \"finding\": \"KIRREL2 (filtrin) is a type I transmembrane protein with five Ig domains, one transmembrane domain, and an intracellular domain, belonging to the immunoglobulin superfamily with structural homology to nephrin, NEPH1, and Drosophila RST. Expression is predominantly in pancreatic beta cells and also in the nervous system.\",\n      \"method\": \"Computational gene discovery, RT-PCR, Northern blot, immunohistochemistry\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple orthogonal methods (computational, RT-PCR, Northern blot, IHC) from a single lab establishing basic structural identity and expression pattern\",\n      \"pmids\": [\"12837264\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Filtrin (KIRREL2/NEPH3) is expressed in kidney glomeruli and localizes to the slit diaphragm region, and immunoblotting detects a specific band at ~107 kDa in human and rat glomeruli, consistent with its proposed role as a component of the glomerular filtration barrier.\",\n      \"method\": \"RT-PCR, immunoblotting, immunofluorescence microscopy\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple orthogonal methods (RT-PCR, Western blot, immunofluorescence) in a single lab establishing localization\",\n      \"pmids\": [\"12504092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Filtrin (KIRREL2/NEPH3) localizes to the slit diaphragm of podocyte foot processes by immunoelectron microscopy, and its mRNA and protein expression are down-regulated in human proteinuric glomerular diseases including focal segmental glomerulosclerosis.\",\n      \"method\": \"Quantitative RT-PCR, immunofluorescence microscopy, immunoelectron microscopy\",\n      \"journal\": \"Nephrology, dialysis, transplantation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — immunoelectron microscopy directly localizes protein to slit diaphragm; multiple orthogonal methods in single lab\",\n      \"pmids\": [\"17442742\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Ptf1a transcription factor directly controls expression of Neph3 (KIRREL2) by binding to a PTF-binding motif in the 5'-flanking region of the Neph3 gene and activating transcription; Neph3 expression is lost in Ptf1a-null mice and induced by ectopic Ptf1a expression. Additionally, Neph3 interacts homophilically and heterophilically with Nephrin.\",\n      \"method\": \"ChIP, promoter reporter assay, in vivo Ptf1a knockout mice, ectopic Ptf1a expression, co-immunoprecipitation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (ChIP, reporter assay, KO mice, ectopic expression, co-IP) establishing direct transcriptional regulation and protein-protein interaction\",\n      \"pmids\": [\"19887377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Neph3 (KIRREL2) is a direct downstream target gene of Ptf1a in cerebellar GABAergic progenitors, marking the ventricular zone progenitors that give rise to Purkinje cells. Neph3+ E-cadherin-high cells are PC progenitors while Neph3+ E-cadherin-low cells are interneuron progenitors.\",\n      \"method\": \"FACS sorting, in vitro cell fate assay, in vivo lineage tracing with Neph3 promoter-driven GFP transgenic mice, short-term in vivo tracing\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (FACS, in vitro fate mapping, in vivo lineage tracing) from a single lab robustly establishing Neph3 as a cell-fate marker and direct Ptf1a target in cerebellum\",\n      \"pmids\": [\"20004188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"NF-κB and Sp1 transcription factors are key regulators of basal Neph3 (KIRREL2) expression in podocytes: they bind to response elements in the proximal Neph3 promoter (-105 to -57), are essential for basal transcriptional activity by mutational screening, and overexpression of NF-κB increases endogenous Neph3 gene expression.\",\n      \"method\": \"Promoter reporter gene constructs, site-directed mutagenesis, co-transfection, chromatin immunoprecipitation in cultured human podocytes\",\n      \"journal\": \"BMC molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (reporter assay, mutagenesis, ChIP, co-transfection with endogenous read-out) in a single lab\",\n      \"pmids\": [\"19703278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Neph3 (KIRREL2) homodimerizes and heterodimerizes with nephrin and Neph1. Neph3 alone can induce cell adhesion in L fibroblasts that lack endogenous adhesion activity. Nephrin requires trans-interaction with Neph1 or Neph3 to promote cell-cell contact formation. Trans-interaction of nephrin with Neph3 leads to down-regulation of nephrin tyrosine phosphorylation.\",\n      \"method\": \"Co-immunoprecipitation, L fibroblast cell adhesion assay, tyrosine phosphorylation analysis\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — co-IP establishing dimerization partners, functional cell adhesion assay in heterologous system, phosphorylation readout; multiple orthogonal methods in single lab\",\n      \"pmids\": [\"21306299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"WT1 and NF-κB synergistically activate the Neph3 (KIRREL2) gene promoter in podocytes; WT1 and NF-κB physically interact with each other, and TNF-α increases Neph3 mRNA expression via NF-κB. DNA methylation silences Neph3 expression in a cell-type and differentiation stage-dependent manner.\",\n      \"method\": \"Reporter gene assay, chromatin immunoprecipitation, co-immunoprecipitation, overexpression studies, TNF-α treatment with pathway inhibitor, 5-aza-2'-deoxycytidine demethylation treatment, quantitative PCR\",\n      \"journal\": \"Nephrology, dialysis, transplantation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (ChIP, Co-IP, reporter assay, pharmacological treatments with quantitative readouts) in a single lab\",\n      \"pmids\": [\"21980157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Morpholino knockdown of neph3 in zebrafish results in altered glomerular morphology, dilated pronephric tubules, pericardial edema, distorted body curvature, and aberrant brain morphology; the pericardial edema/body curvature phenotype is rescued by wild-type neph3 mRNA, establishing a direct functional role for Neph3 in glomerular and neural development.\",\n      \"method\": \"Antisense morpholino oligonucleotide knockdown in zebrafish, histology, mRNA rescue experiment\",\n      \"journal\": \"Differentiation; research in biological diversity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — morpholino loss-of-function with mRNA rescue in zebrafish, single lab\",\n      \"pmids\": [\"22099175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The NEPH3 variant V353M (KIRREL2) disrupts Neph3 homodimerization and Neph3-Nephrin heterodimerization and is associated with differential activation of the unfolded protein response pathway when overexpressed in stressed podocyte cells, indicating that this variant impairs normal protein-protein interactions and protein folding.\",\n      \"method\": \"Functional dimerization assay, unfolded protein response pathway assay in cultured podocyte cells, genetic association study\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional dimerization and UPR assays in cell culture with a disease variant, single lab\",\n      \"pmids\": [\"28334007\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Kirrel2 is required for axonal coalescence of MOR174-9- and M72-expressing olfactory sensory neurons (OSNs) projecting to the DII region of the olfactory bulb; loss of Kirrel2 causes these OSN axons to target ectopic glomeruli. Kirrel2 and Kirrel3 are dispensable for OSN axon coalescence in the most dorsal (DI) region, indicating region-specific requirements.\",\n      \"method\": \"Kirrel2 knockout mice (loss-of-function), double Kirrel2/Kirrel3 knockout, examination of axonal projections of specific OSN populations\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic KO with defined cellular phenotype (ectopic glomeruli), double KO for epistasis, multiple OSN populations examined\",\n      \"pmids\": [\"31142543\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Filtrin (KIRREL2/NEPH3) is expressed at the gene and protein level in Langerhans islets of the pancreas, co-localizing with beta cell markers, establishing its presence in a second epithelial structure (pancreatic islets) analogous to its podocyte slit diaphragm expression.\",\n      \"method\": \"RT-PCR, immunoblotting, immunofluorescence\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple orthogonal localization methods (RT-PCR, Western, IF) in single lab establishing expression/localization in pancreatic islets\",\n      \"pmids\": [\"16841182\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"KIRREL2 (NEPH3/filtrin) is an immunoglobulin superfamily transmembrane cell adhesion molecule that localizes to the slit diaphragm of kidney podocytes and is transcriptionally regulated by Ptf1a, NF-κB, Sp1, WT1, and DNA methylation; it forms homo- and heterodimers with nephrin and Neph1, promotes cell-cell adhesion in trans, and down-regulates nephrin tyrosine phosphorylation upon contact formation; in the nervous system, it is a direct Ptf1a target marking cerebellar GABAergic progenitors and is required for proper olfactory sensory neuron axon coalescence into glomeruli in the DII region of the olfactory bulb.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"KIRREL2 (NEPH3/filtrin) is an immunoglobulin-superfamily type I transmembrane cell-adhesion molecule with five extracellular Ig domains that functions at specialized cell-cell junctions in epithelia and in neural circuit assembly [#0]. In the kidney it localizes to the slit diaphragm of podocyte foot processes, where it engages in homophilic and heterophilic trans-interactions with nephrin and Neph1 to mediate cell-cell adhesion, and its trans-engagement with nephrin down-regulates nephrin tyrosine phosphorylation, linking contact formation to signaling at the filtration barrier [#2, #3, #6]. Its expression is controlled by a convergent transcriptional program: Ptf1a binds the 5'-flanking region to directly activate transcription, NF-\\u03baB and Sp1 drive basal promoter activity, WT1 synergizes with NF-\\u03baB, and DNA methylation silences the gene in a stage- and cell-type-dependent manner [#3, #5, #7]. Beyond the kidney, KIRREL2 is a direct Ptf1a target that marks cerebellar GABAergic ventricular-zone progenitors and is required for region-specific coalescence of olfactory sensory neuron axons into glomeruli in the DII domain of the olfactory bulb, with loss of function producing ectopic glomerular targeting [#4, #10]. A V353M variant that disrupts both homo- and heterodimerization and perturbs the unfolded protein response connects its adhesive function to podocyte disease [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Establishing the molecular identity of KIRREL2 was the first step: it was unknown what kind of protein it was, and structural characterization placed it as a nephrin/NEPH1-related Ig-superfamily adhesion molecule expressed in pancreatic beta cells and nervous system.\",\n      \"evidence\": \"Computational gene discovery with RT-PCR, Northern blot and immunohistochemistry\",\n      \"pmids\": [\"12837264\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not establish binding partners or function\", \"Tissue expression survey only, no mechanism\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Localizing the protein answered where it acts: immunolocalization placed filtrin at the glomerular slit diaphragm, implicating it as a component of the filtration barrier.\",\n      \"evidence\": \"RT-PCR, immunoblotting and immunofluorescence in human and rat glomeruli\",\n      \"pmids\": [\"12504092\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Light-level localization only; ultrastructural placement not yet shown\", \"Functional contribution to filtration untested\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Whether KIRREL2 acts only at the slit diaphragm was addressed by showing it is also expressed in pancreatic islet beta cells, extending its association to a second specialized epithelial structure.\",\n      \"evidence\": \"RT-PCR, immunoblotting and immunofluorescence in pancreatic Langerhans islets\",\n      \"pmids\": [\"16841182\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role in islets not determined\", \"No partner or signaling data in beta cells\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Ultrastructural localization and disease correlation refined the role: immunoelectron microscopy confirmed slit-diaphragm placement and showed down-regulation in human proteinuric disease, linking KIRREL2 to barrier integrity.\",\n      \"evidence\": \"Quantitative RT-PCR, immunofluorescence and immunoelectron microscopy in normal and FSGS human glomeruli\",\n      \"pmids\": [\"17442742\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Correlation not causation in human disease\", \"Mechanism of down-regulation unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"How KIRREL2 expression is controlled and what it binds were answered together: Ptf1a directly activates the gene via a promoter motif, and KIRREL2 interacts homo- and heterophilically with nephrin, establishing both an upstream regulator and a physical adhesion partner.\",\n      \"evidence\": \"ChIP, promoter reporter assays, Ptf1a-null mice, ectopic expression, and co-immunoprecipitation\",\n      \"pmids\": [\"19887377\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of nephrin interaction not yet defined\", \"Other transcriptional inputs not assessed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"The neural role was identified: lineage tracing showed KIRREL2 is a direct Ptf1a target marking cerebellar GABAergic ventricular-zone progenitors, distinguishing Purkinje cell from interneuron progenitor pools by E-cadherin level.\",\n      \"evidence\": \"FACS, in vitro fate assays and in vivo lineage tracing with Neph3 promoter-GFP transgenic mice\",\n      \"pmids\": [\"20004188\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"KIRREL2 used as marker; its functional requirement in cerebellar fate not tested\", \"Adhesive mechanism in progenitors unaddressed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"The basal transcriptional machinery was defined: NF-\\u03baB and Sp1 bind the proximal promoter and are essential for basal activity in podocytes, identifying the core regulators of constitutive expression.\",\n      \"evidence\": \"Promoter reporter constructs, site-directed mutagenesis, ChIP and co-transfection in cultured human podocytes\",\n      \"pmids\": [\"19703278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signal inputs controlling these factors not defined\", \"Cell-type specificity of regulation not explained\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"The mechanistic role of the interactions was established: KIRREL2 homo- and heterodimerizes with nephrin and Neph1, can drive adhesion autonomously in fibroblasts, and its trans-engagement of nephrin down-regulates nephrin tyrosine phosphorylation, coupling adhesion to signaling.\",\n      \"evidence\": \"Co-immunoprecipitation, L fibroblast adhesion assay and tyrosine phosphorylation analysis\",\n      \"pmids\": [\"21306299\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Phosphatase/kinase mediating dephosphorylation not identified\", \"In vivo relevance of phosphorylation control not demonstrated\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Transcriptional control was integrated: WT1 synergizes with NF-\\u03baB, TNF-\\u03b1 induces expression via NF-\\u03baB, and DNA methylation silences the gene, showing combinatorial and epigenetic regulation.\",\n      \"evidence\": \"Reporter assays, ChIP, co-IP, TNF-\\u03b1 treatment with pathway inhibitor, and 5-aza-2'-deoxycytidine demethylation with qPCR\",\n      \"pmids\": [\"21980157\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological trigger for methylation changes not defined\", \"Interplay with Ptf1a not reconciled\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"In vivo requirement was tested: morpholino knockdown of neph3 in zebrafish produced glomerular and neural defects rescued by wild-type mRNA, providing loss-of-function evidence for a developmental role.\",\n      \"evidence\": \"Antisense morpholino knockdown in zebrafish with histology and mRNA rescue\",\n      \"pmids\": [\"22099175\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Morpholino specificity caveats\", \"Cellular mechanism behind phenotypes not resolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"A disease-linked variant connected dimerization to pathology: V353M disrupts homo- and heterodimerization and alters the unfolded protein response, mechanistically linking impaired KIRREL2 interactions to podocyte dysfunction.\",\n      \"evidence\": \"Functional dimerization and UPR assays in cultured podocytes with genetic association\",\n      \"pmids\": [\"28334007\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causality in patient kidney disease not established\", \"Single variant in cell-culture overexpression\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"A definitive in vivo neural function was shown: Kirrel2 knockout mice display ectopic glomerular targeting of specific olfactory sensory neuron populations in the DII region, establishing a region-specific role in axon coalescence.\",\n      \"evidence\": \"Kirrel2 single and Kirrel2/Kirrel3 double knockout mice with analysis of defined OSN axon projections\",\n      \"pmids\": [\"31142543\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular partners of KIRREL2 in OSN axons not identified\", \"Mechanism of regional specificity unexplained\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how KIRREL2's adhesion and signaling functions are mechanistically deployed across its different tissues, including its functional role in pancreatic beta cells and the downstream effectors linking trans-adhesion to nephrin dephosphorylation in vivo.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No identified phosphatase mediating nephrin dephosphorylation\", \"Beta-cell function uncharacterized\", \"Cytoplasmic effectors of KIRREL2 signaling not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [3, 6]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4, 10]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [3, 5, 7]}\n    ],\n    \"complexes\": [\"slit diaphragm\"],\n    \"partners\": [\"NPHS1\", \"KIRREL1\", \"PTF1A\", \"WT1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":4,"faith_total":5,"faith_pct":80.0}}