{"gene":"TMEM25","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2023,"finding":"TMEM25 physically associates with monomeric EGFR and suppresses ligand-independent EGFR monomer-mediated phosphorylation of STAT3 at basal state; loss of TMEM25 allows monomeric EGFR to phosphorylate STAT3 independently of ligand binding, enhancing basal STAT3 activation and promoting TNBC progression. AAV-mediated TMEM25 restoration suppressed STAT3 activation in vivo.","method":"Co-immunoprecipitation, loss-of-function (TMEM25-KO cells and mice), AAV overexpression rescue, phospho-STAT3 immunoblotting, electrophysiology","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP establishing direct interaction, KO phenotype with defined molecular readout (STAT3 phosphorylation), in vivo AAV rescue, replicated across multiple orthogonal methods in one rigorous study","pmids":["37095176"],"is_preprint":false},{"year":2019,"finding":"TMEM25 localizes to late endosomes in neurons, physically interacts with the NMDA receptor NR2B subunit (co-localized to late endosome compartments), induces acidification changes in lysosome compartments, and accelerates lysosomal degradation of NR2B, thereby modulating neuronal excitability. TMEM25 overexpression attenuated epileptic seizure phenotypes while knockdown exacerbated them.","method":"Subcellular fractionation/immunofluorescence co-localization to late endosomes, Co-immunoprecipitation (TMEM25–NR2B interaction), lysosomal pH assays, Western blot for NR2B protein levels, electrophysiology, in vivo KD/OE in epilepsy mouse models","journal":"The Journal of Clinical Investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, direct localization with functional consequence (lysosomal degradation of NR2B), multiple orthogonal methods (electrophysiology, pH assay, protein turnover, in vivo behavioral rescue) in a single rigorous study","pmids":["31424425"],"is_preprint":false},{"year":2023,"finding":"TMEM25 localizes to tight junctions in epithelial cells and binds Par3 via a PDZ-mediated interaction with its C-terminal cytoplasmic tail. Via its N-terminal extracellular domain, TMEM25 associates with claudin-1 and claudin-2 and suppresses their cis- and trans-oligomerizations, thereby attenuating tight junction strand formation. Par3 binding to TMEM25 attenuates TMEM25–claudin association, modulating claudin oligomerization. Depletion of TMEM25 accelerates TJ development, while overexpression (but not C-terminally deleted mutant) delays it.","method":"Immunofluorescence localization to tight junctions, Co-immunoprecipitation (TMEM25–Par3 and TMEM25–claudin-1/2), domain deletion mutagenesis (C-terminal and N-terminal truncations), siRNA knockdown and overexpression with TJ assembly kinetics assay, claudin oligomerization assays","journal":"EMBO Reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP for multiple partners, domain mutagenesis establishing structure-function, direct localization with functional consequence (TJ assembly kinetics), multiple orthogonal methods in one study","pmids":["38177906"],"is_preprint":false},{"year":2023,"finding":"TMEM25 overexpression in mouse ventricular cortical progenitors promoted proliferation of basal radial glia (bRG) and increased upper-layer neuron numbers in vivo. Knockdown of TMEM25 in human neural progenitor cells inhibited cell cycle progression via repression of Akt signaling, suggesting TMEM25 receives extracellular signals to promote NPC expansion through an Akt-dependent pathway.","method":"In vitro NPC proliferation assays (overexpression), in vivo mouse cortical electroporation (bRG expansion, upper-layer neuron counting), TMEM25 knockdown in human NPCs with RNA-seq and pharmacological Akt pathway assays","journal":"FEBS Letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo and in vitro gain/loss-of-function with defined cellular phenotypes and Akt pathway readout, single lab, pathway placement inferred from pharmacological assay rather than direct biochemical reconstitution","pmids":["37846797"],"is_preprint":false},{"year":2013,"finding":"CpG island hypermethylation of TMEM25 is inversely correlated with reduced TMEM25 expression in colorectal cancer tissue, demonstrating that epigenetic silencing via DNA methylation is a mechanism of TMEM25 downregulation in cancer.","method":"Whole-genome methylation scan, methylation-specific high-resolution melting analysis (133 CRC samples), expression quantification by RT-PCR, correlation analysis of methylation vs. expression","journal":"Disease Markers","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct correlation of methylation with expression loss across large sample set, single lab, no functional manipulation of methylation to confirm causal role","pmids":["23324576"],"is_preprint":false},{"year":2004,"finding":"TMEM25 was identified as a member of the immunoglobulin superfamily containing a C-2 type immunoglobulin domain (codons 42–112). The gene encodes two isoforms by alternative exon skipping: isoform 1 (366 aa, transmembrane) and isoform 2 (322 aa, secreted). Human TMEM25 shares 91% amino acid identity with mouse Tmem25.","method":"In silico bioinformatics analysis of cDNA sequences (BC042896, AY358919, AK002841), domain homology prediction","journal":"Oncology Reports","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no experimental validation of protein domains or isoform function","pmids":["15254712"],"is_preprint":false}],"current_model":"TMEM25 is a single-pass transmembrane immunoglobulin superfamily protein that acts as a negative regulator in multiple signaling contexts: it physically associates with monomeric EGFR to suppress ligand-independent EGFR–STAT3 signaling in breast cancer cells; in neurons it localizes to late endosomes, binds NMDA receptor subunit NR2B, and promotes its lysosomal degradation to dampen neuronal excitability; in epithelial cells it localizes to tight junctions, binds Par3 via a PDZ interaction and claudin-1/2 via its extracellular domain to attenuate claudin oligomerization and TJ strand formation; and in neural progenitors it promotes Akt-dependent cell cycle progression to support cortical expansion."},"narrative":{"mechanistic_narrative":"TMEM25 is a single-pass transmembrane immunoglobulin-superfamily protein that functions as a negative regulator of receptor signaling across epithelial, neuronal, and tumor contexts [PMID:37095176, PMID:31424425, PMID:38177906]. In triple-negative breast cancer cells it physically associates with monomeric EGFR and suppresses ligand-independent EGFR-mediated phosphorylation of STAT3; its loss permits basal STAT3 activation and tumor progression, and AAV-mediated restoration reverses this in vivo [PMID:37095176]. In neurons TMEM25 localizes to late endosomes, binds the NMDA receptor subunit NR2B, and accelerates its lysosomal degradation, thereby dampening neuronal excitability and constraining seizure phenotypes [PMID:31424425]. In epithelial cells it localizes to tight junctions, where its C-terminal cytoplasmic tail engages Par3 through a PDZ interaction while its N-terminal extracellular domain binds claudin-1 and claudin-2 to suppress claudin cis- and trans-oligomerization and attenuate tight-junction strand formation; Par3 binding in turn weakens the TMEM25–claudin association [PMID:38177906]. A distinct role in neural progenitors couples TMEM25 to Akt-dependent cell cycle progression supporting cortical expansion [PMID:37846797]. TMEM25 is epigenetically silenced by CpG island hypermethylation in colorectal cancer, consistent with a tumor-suppressive function [PMID:23324576].","teleology":[{"year":2013,"claim":"Established that TMEM25 expression is lost in cancer through a defined epigenetic mechanism, framing it as a candidate tumor suppressor before any molecular function was known.","evidence":"Whole-genome methylation scan and methylation-specific melting analysis correlated with RT-PCR expression across 133 colorectal cancer samples","pmids":["23324576"],"confidence":"Medium","gaps":["No functional manipulation of methylation to prove causality","No molecular function for TMEM25 defined at this stage","Tumor-suppressive role inferred from correlation only"]},{"year":2019,"claim":"Defined the first mechanistic role for TMEM25 by showing it drives lysosomal turnover of an NMDA receptor subunit, answering how it controls neuronal excitability.","evidence":"Late-endosome co-localization, reciprocal Co-IP with NR2B, lysosomal pH assays, NR2B turnover Western blots, electrophysiology, and in vivo epilepsy models with knockdown/overexpression","pmids":["31424425"],"confidence":"High","gaps":["Mechanism by which TMEM25 targets NR2B to lysosomes is not resolved","Whether TMEM25 directly alters lysosomal acidification or acts indirectly is unclear"]},{"year":2023,"claim":"Showed TMEM25 restrains ligand-independent EGFR–STAT3 signaling, explaining how its loss promotes tumor progression and tying the methylation silencing to a concrete oncogenic pathway.","evidence":"Reciprocal Co-IP with monomeric EGFR, TMEM25-KO cells and mice, phospho-STAT3 immunoblotting, and AAV rescue in vivo","pmids":["37095176"],"confidence":"High","gaps":["Structural basis for TMEM25 selectivity for monomeric versus dimeric EGFR not defined","Whether the EGFR-suppressive role generalizes beyond TNBC is untested"]},{"year":2023,"claim":"Resolved how TMEM25 modulates epithelial barrier assembly by mapping distinct extracellular (claudin) and cytoplasmic (Par3/PDZ) interactions to tight-junction strand formation.","evidence":"Tight-junction immunofluorescence, reciprocal Co-IP for Par3 and claudin-1/2, domain-deletion mutagenesis, claudin oligomerization assays, and TJ assembly kinetics under knockdown/overexpression","pmids":["38177906"],"confidence":"High","gaps":["How the three signaling roles (EGFR, NR2B, claudin/Par3) relate within a single cell is unknown","Stoichiometry of the TMEM25–claudin–Par3 interplay not quantified"]},{"year":2023,"claim":"Linked TMEM25 to neural progenitor proliferation via Akt signaling, indicating a developmental role distinct from its suppressive functions elsewhere.","evidence":"In vitro NPC proliferation assays, in vivo mouse cortical electroporation with bRG and upper-layer neuron counting, and knockdown in human NPCs with RNA-seq and pharmacological Akt readouts","pmids":["37846797"],"confidence":"Medium","gaps":["Akt pathway placement is pharmacological, not biochemically reconstituted","Upstream extracellular signal and direct receptor are not identified","Single-lab finding"]},{"year":null,"claim":"It remains unknown whether TMEM25's context-specific roles share a unifying biochemical activity or reflect independent partner-dependent functions.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structure of TMEM25 or its complexes","No unifying biochemical activity assigned to the Ig domain","Relationship between endosomal, tight-junction, and EGFR roles unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,3]},{"term_id":"R-HSA-1500931","term_label":"Cell-Cell communication","supporting_discovery_ids":[2]}],"complexes":[],"partners":["EGFR","GRIN2B","PARD3","CLDN1","CLDN2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86YD3","full_name":"Transmembrane protein 25","aliases":[],"length_aa":366,"mass_kda":39.3,"function":"In neurons, modulates the degradation of NMDA receptor GRIN2B subunit. Plays a role in the regulation of neuronal excitability","subcellular_location":"Late endosome; Lysosome","url":"https://www.uniprot.org/uniprotkb/Q86YD3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TMEM25","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TMEM25","total_profiled":1310},"omim":[{"mim_id":"613934","title":"TRANSMEMBRANE PROTEIN 25; TMEM25","url":"https://www.omim.org/entry/613934"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TMEM25"},"hgnc":{"alias_symbol":["FLJ14399"],"prev_symbol":[]},"alphafold":{"accession":"Q86YD3","domains":[{"cath_id":"2.60.40.10","chopping":"31-128","consensus_level":"medium","plddt":86.0526,"start":31,"end":128},{"cath_id":"2.60.40,2.60.40","chopping":"130-221","consensus_level":"medium","plddt":62.1468,"start":130,"end":221}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86YD3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86YD3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86YD3-F1-predicted_aligned_error_v6.png","plddt_mean":62.84},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMEM25","jax_strain_url":"https://www.jax.org/strain/search?query=TMEM25"},"sequence":{"accession":"Q86YD3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86YD3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86YD3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86YD3"}},"corpus_meta":[{"pmid":"37095176","id":"PMC_37095176","title":"TMEM25 inhibits monomeric EGFR-mediated STAT3 activation in basal state to suppress triple-negative breast cancer progression.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/37095176","citation_count":52,"is_preprint":false},{"pmid":"23324576","id":"PMC_23324576","title":"TMEM25 is a candidate biomarker methylated and down-regulated in colorectal cancer.","date":"2013","source":"Disease markers","url":"https://pubmed.ncbi.nlm.nih.gov/23324576","citation_count":51,"is_preprint":false},{"pmid":"31424425","id":"PMC_31424425","title":"TMEM25 modulates neuronal excitability and NMDA receptor subunit NR2B degradation.","date":"2019","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/31424425","citation_count":26,"is_preprint":false},{"pmid":"15254712","id":"PMC_15254712","title":"Identification and characterization of human TMEM25 and mouse Tmem25 genes in silico.","date":"2004","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/15254712","citation_count":17,"is_preprint":false},{"pmid":"29256224","id":"PMC_29256224","title":"[Effects of lncRNA RP11-770J1.3 and TMEM25 expression on paclitaxel resistance in human breast cancer cells].","date":"2017","source":"Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/29256224","citation_count":14,"is_preprint":false},{"pmid":"33936159","id":"PMC_33936159","title":"Meta-Analyses of Splicing and Expression Quantitative Trait Loci Identified Susceptibility Genes of Glioma.","date":"2021","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33936159","citation_count":11,"is_preprint":false},{"pmid":"35991532","id":"PMC_35991532","title":"Whole Exome Sequencing in Two Southeast Asian Families With Atypical Femur Fractures.","date":"2022","source":"JBMR plus","url":"https://pubmed.ncbi.nlm.nih.gov/35991532","citation_count":7,"is_preprint":false},{"pmid":"38177906","id":"PMC_38177906","title":"TMEM25 is a Par3-binding protein that attenuates claudin assembly during tight junction development.","date":"2023","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/38177906","citation_count":5,"is_preprint":false},{"pmid":"38189809","id":"PMC_38189809","title":"Multidimensional comprehensive and integrated analysis of the potential function of TMEM25 in renal clear cell carcinoma with low expression status.","date":"2024","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/38189809","citation_count":3,"is_preprint":false},{"pmid":"38532948","id":"PMC_38532948","title":"Transmembrane protein 25 abrogates monomeric EGFR-driven STAT3 activation in triple-negative breast cancer.","date":"2024","source":"MedComm","url":"https://pubmed.ncbi.nlm.nih.gov/38532948","citation_count":3,"is_preprint":false},{"pmid":"37846797","id":"PMC_37846797","title":"Human-biased TMEM25 expression promotes expansion of neural progenitor cells to alter cortical structure in the developing brain.","date":"2023","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/37846797","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7511,"output_tokens":1950,"usd":0.025892,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8875,"output_tokens":2411,"usd":0.052325,"stage2_stop_reason":"end_turn"},"total_usd":0.078217,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"TMEM25 physically associates with monomeric EGFR and suppresses ligand-independent EGFR monomer-mediated phosphorylation of STAT3 at basal state; loss of TMEM25 allows monomeric EGFR to phosphorylate STAT3 independently of ligand binding, enhancing basal STAT3 activation and promoting TNBC progression. AAV-mediated TMEM25 restoration suppressed STAT3 activation in vivo.\",\n      \"method\": \"Co-immunoprecipitation, loss-of-function (TMEM25-KO cells and mice), AAV overexpression rescue, phospho-STAT3 immunoblotting, electrophysiology\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP establishing direct interaction, KO phenotype with defined molecular readout (STAT3 phosphorylation), in vivo AAV rescue, replicated across multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"37095176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TMEM25 localizes to late endosomes in neurons, physically interacts with the NMDA receptor NR2B subunit (co-localized to late endosome compartments), induces acidification changes in lysosome compartments, and accelerates lysosomal degradation of NR2B, thereby modulating neuronal excitability. TMEM25 overexpression attenuated epileptic seizure phenotypes while knockdown exacerbated them.\",\n      \"method\": \"Subcellular fractionation/immunofluorescence co-localization to late endosomes, Co-immunoprecipitation (TMEM25–NR2B interaction), lysosomal pH assays, Western blot for NR2B protein levels, electrophysiology, in vivo KD/OE in epilepsy mouse models\",\n      \"journal\": \"The Journal of Clinical Investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, direct localization with functional consequence (lysosomal degradation of NR2B), multiple orthogonal methods (electrophysiology, pH assay, protein turnover, in vivo behavioral rescue) in a single rigorous study\",\n      \"pmids\": [\"31424425\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TMEM25 localizes to tight junctions in epithelial cells and binds Par3 via a PDZ-mediated interaction with its C-terminal cytoplasmic tail. Via its N-terminal extracellular domain, TMEM25 associates with claudin-1 and claudin-2 and suppresses their cis- and trans-oligomerizations, thereby attenuating tight junction strand formation. Par3 binding to TMEM25 attenuates TMEM25–claudin association, modulating claudin oligomerization. Depletion of TMEM25 accelerates TJ development, while overexpression (but not C-terminally deleted mutant) delays it.\",\n      \"method\": \"Immunofluorescence localization to tight junctions, Co-immunoprecipitation (TMEM25–Par3 and TMEM25–claudin-1/2), domain deletion mutagenesis (C-terminal and N-terminal truncations), siRNA knockdown and overexpression with TJ assembly kinetics assay, claudin oligomerization assays\",\n      \"journal\": \"EMBO Reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP for multiple partners, domain mutagenesis establishing structure-function, direct localization with functional consequence (TJ assembly kinetics), multiple orthogonal methods in one study\",\n      \"pmids\": [\"38177906\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TMEM25 overexpression in mouse ventricular cortical progenitors promoted proliferation of basal radial glia (bRG) and increased upper-layer neuron numbers in vivo. Knockdown of TMEM25 in human neural progenitor cells inhibited cell cycle progression via repression of Akt signaling, suggesting TMEM25 receives extracellular signals to promote NPC expansion through an Akt-dependent pathway.\",\n      \"method\": \"In vitro NPC proliferation assays (overexpression), in vivo mouse cortical electroporation (bRG expansion, upper-layer neuron counting), TMEM25 knockdown in human NPCs with RNA-seq and pharmacological Akt pathway assays\",\n      \"journal\": \"FEBS Letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo and in vitro gain/loss-of-function with defined cellular phenotypes and Akt pathway readout, single lab, pathway placement inferred from pharmacological assay rather than direct biochemical reconstitution\",\n      \"pmids\": [\"37846797\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"CpG island hypermethylation of TMEM25 is inversely correlated with reduced TMEM25 expression in colorectal cancer tissue, demonstrating that epigenetic silencing via DNA methylation is a mechanism of TMEM25 downregulation in cancer.\",\n      \"method\": \"Whole-genome methylation scan, methylation-specific high-resolution melting analysis (133 CRC samples), expression quantification by RT-PCR, correlation analysis of methylation vs. expression\",\n      \"journal\": \"Disease Markers\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct correlation of methylation with expression loss across large sample set, single lab, no functional manipulation of methylation to confirm causal role\",\n      \"pmids\": [\"23324576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"TMEM25 was identified as a member of the immunoglobulin superfamily containing a C-2 type immunoglobulin domain (codons 42–112). The gene encodes two isoforms by alternative exon skipping: isoform 1 (366 aa, transmembrane) and isoform 2 (322 aa, secreted). Human TMEM25 shares 91% amino acid identity with mouse Tmem25.\",\n      \"method\": \"In silico bioinformatics analysis of cDNA sequences (BC042896, AY358919, AK002841), domain homology prediction\",\n      \"journal\": \"Oncology Reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no experimental validation of protein domains or isoform function\",\n      \"pmids\": [\"15254712\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TMEM25 is a single-pass transmembrane immunoglobulin superfamily protein that acts as a negative regulator in multiple signaling contexts: it physically associates with monomeric EGFR to suppress ligand-independent EGFR–STAT3 signaling in breast cancer cells; in neurons it localizes to late endosomes, binds NMDA receptor subunit NR2B, and promotes its lysosomal degradation to dampen neuronal excitability; in epithelial cells it localizes to tight junctions, binds Par3 via a PDZ interaction and claudin-1/2 via its extracellular domain to attenuate claudin oligomerization and TJ strand formation; and in neural progenitors it promotes Akt-dependent cell cycle progression to support cortical expansion.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TMEM25 is a single-pass transmembrane immunoglobulin-superfamily protein that functions as a negative regulator of receptor signaling across epithelial, neuronal, and tumor contexts [#0, #1, #2]. In triple-negative breast cancer cells it physically associates with monomeric EGFR and suppresses ligand-independent EGFR-mediated phosphorylation of STAT3; its loss permits basal STAT3 activation and tumor progression, and AAV-mediated restoration reverses this in vivo [#0]. In neurons TMEM25 localizes to late endosomes, binds the NMDA receptor subunit NR2B, and accelerates its lysosomal degradation, thereby dampening neuronal excitability and constraining seizure phenotypes [#1]. In epithelial cells it localizes to tight junctions, where its C-terminal cytoplasmic tail engages Par3 through a PDZ interaction while its N-terminal extracellular domain binds claudin-1 and claudin-2 to suppress claudin cis- and trans-oligomerization and attenuate tight-junction strand formation; Par3 binding in turn weakens the TMEM25–claudin association [#2]. A distinct role in neural progenitors couples TMEM25 to Akt-dependent cell cycle progression supporting cortical expansion [#3]. TMEM25 is epigenetically silenced by CpG island hypermethylation in colorectal cancer, consistent with a tumor-suppressive function [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established that TMEM25 expression is lost in cancer through a defined epigenetic mechanism, framing it as a candidate tumor suppressor before any molecular function was known.\",\n      \"evidence\": \"Whole-genome methylation scan and methylation-specific melting analysis correlated with RT-PCR expression across 133 colorectal cancer samples\",\n      \"pmids\": [\"23324576\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No functional manipulation of methylation to prove causality\", \"No molecular function for TMEM25 defined at this stage\", \"Tumor-suppressive role inferred from correlation only\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined the first mechanistic role for TMEM25 by showing it drives lysosomal turnover of an NMDA receptor subunit, answering how it controls neuronal excitability.\",\n      \"evidence\": \"Late-endosome co-localization, reciprocal Co-IP with NR2B, lysosomal pH assays, NR2B turnover Western blots, electrophysiology, and in vivo epilepsy models with knockdown/overexpression\",\n      \"pmids\": [\"31424425\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Mechanism by which TMEM25 targets NR2B to lysosomes is not resolved\", \"Whether TMEM25 directly alters lysosomal acidification or acts indirectly is unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed TMEM25 restrains ligand-independent EGFR–STAT3 signaling, explaining how its loss promotes tumor progression and tying the methylation silencing to a concrete oncogenic pathway.\",\n      \"evidence\": \"Reciprocal Co-IP with monomeric EGFR, TMEM25-KO cells and mice, phospho-STAT3 immunoblotting, and AAV rescue in vivo\",\n      \"pmids\": [\"37095176\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Structural basis for TMEM25 selectivity for monomeric versus dimeric EGFR not defined\", \"Whether the EGFR-suppressive role generalizes beyond TNBC is untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Resolved how TMEM25 modulates epithelial barrier assembly by mapping distinct extracellular (claudin) and cytoplasmic (Par3/PDZ) interactions to tight-junction strand formation.\",\n      \"evidence\": \"Tight-junction immunofluorescence, reciprocal Co-IP for Par3 and claudin-1/2, domain-deletion mutagenesis, claudin oligomerization assays, and TJ assembly kinetics under knockdown/overexpression\",\n      \"pmids\": [\"38177906\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"How the three signaling roles (EGFR, NR2B, claudin/Par3) relate within a single cell is unknown\", \"Stoichiometry of the TMEM25–claudin–Par3 interplay not quantified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Linked TMEM25 to neural progenitor proliferation via Akt signaling, indicating a developmental role distinct from its suppressive functions elsewhere.\",\n      \"evidence\": \"In vitro NPC proliferation assays, in vivo mouse cortical electroporation with bRG and upper-layer neuron counting, and knockdown in human NPCs with RNA-seq and pharmacological Akt readouts\",\n      \"pmids\": [\"37846797\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Akt pathway placement is pharmacological, not biochemically reconstituted\", \"Upstream extracellular signal and direct receptor are not identified\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether TMEM25's context-specific roles share a unifying biochemical activity or reflect independent partner-dependent functions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No structure of TMEM25 or its complexes\", \"No unifying biochemical activity assigned to the Ig domain\", \"Relationship between endosomal, tight-junction, and EGFR roles unresolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"R-HSA-1500931\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"EGFR\", \"GRIN2B\", \"PARD3\", \"CLDN1\", \"CLDN2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":6,"faith_total":6,"faith_pct":100.0}}