{"gene":"TMED9","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2019,"finding":"BRD4780 binds TMED9 directly, releasing trapped misfolded MUC1-fs cargo from TMED9-containing vesicles of the early secretory pathway and re-routing it for lysosomal degradation; TMED9 deletion phenocopies this effect, establishing TMED9 as a cargo receptor that entraps misfolded proteins in the early secretory pathway.","method":"Small molecule binding assay, patient cell lines, knockin mouse kidneys, patient kidney organoids, TMED9 deletion/knockdown with protein clearance readouts","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (chemical probe, genetic deletion, organoid models), replicated across patient cells and in vivo mouse model","pmids":["31348885"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structures reveal that TMED9 self-oligomerizes into octamers, dodecamers, and higher-order oligomers driven by an intrinsic symmetry mismatch between its trimeric coiled-coil domain and tetrameric transmembrane domain. The luminal Golgi-dynamics domain directly interacts with frameshifted MUC1 cargo. TMED9 oligomerization favors recruitment of COPI (but not COPII) coatomers, facilitating retrograde transport and explaining cargo entrapment.","method":"Cryo-electron microscopy structure determination, domain mutagenesis, COPI/COPII recruitment assays","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with functional validation of COPI/COPII recruitment and cargo interaction, single rigorous study with multiple orthogonal methods","pmids":["39303030"],"is_preprint":false},{"year":2021,"finding":"TMED9 interacts with SEC12 at the ER-Golgi intermediate compartment (ERGIC) to establish a new ERGIC-ERES membrane contact (2–5 nm distance) that transactivates COPII assembly on the ERGIC, promotes formation of ERGIC-derived COPII vesicles, and is required for stress-induced autophagosome biogenesis.","method":"Co-immunoprecipitation, super-resolution and electron microscopy, siRNA knockdown, COPII assembly assays, autophagy flux assays","journal":"Cell research","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal interaction between TMED9 and SEC12 shown with Co-IP, membrane contact quantified by EM, functional consequence confirmed by KD with autophagy readouts","pmids":["34561617"],"is_preprint":false},{"year":2025,"finding":"TMED9 plays a requisite role in the RESET pathway for quality control of misfolded GPI-anchored proteins (GPI-APs): it associates with misfolded GPI-APs (but not wild-type GPI-APs) in the ER after their release from calnexin, and conveys them to the Golgi. siRNA depletion or BRD4780 treatment blocks ER-export of misfolded GPI-APs specifically. Acute BRD4780 treatment shifts TMED9 localization from ER to Golgi cisternae, blocking RESET; removal of BRD4780 restores ER localization and RESET activity.","method":"Biochemical fractionation, co-immunoprecipitation, live-cell imaging, siRNA knockdown, chemical inhibitor (BRD4780) treatment, localization assays","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biochemical and imaging methods in single lab, specific cargo selectivity (misfolded vs. WT) demonstrated","pmids":["40203033"],"is_preprint":false},{"year":2019,"finding":"TMED9 acts downstream of TMED3 in colon cancer cells and promotes pro-metastatic behavior via regulation of TGFα biogenesis and secretion; TMED9 knockdown compromises TGFα biogenesis and impairs cell migration. TMED9 function is linked to CNIH4 (a TGFα exporter) and establishes a positive feedback loop with TGFα and GLI1 that opposes TMED3-WNT-TCF signaling.","method":"siRNA knockdown, functional rescue assays, migration/invasion assays, gene expression analysis across three colon cancer cell lines","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — epistasis and functional rescue in multiple cell lines, but no direct biochemical interaction demonstrated for the TMED9-TGFα-CNIH4 complex","pmids":["31253868"],"is_preprint":false},{"year":2015,"finding":"p24α2 (TMED9) is localized to pre-synaptic terminals in the mammalian brain and is condensed at active zone-docked synaptic vesicles, as established by immunohistochemistry, subcellular fractionation, and synaptic vesicle immunoisolation. Amyloid precursor protein and γ-secretase components co-localize at the same active zone-docked synaptic vesicles.","method":"Immunohistochemistry, subcellular fractionation, synaptic vesicle immunoisolation","journal":"Journal of neurochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — subcellular fractionation and immunoisolation establish localization, single lab with no functional loss-of-function data","pmids":["25438880"],"is_preprint":false},{"year":2021,"finding":"TMED9 interacts with BPIFB3 (identified by proximity-dependent biotinylation/BioID followed by mass spectrometry) and regulates non-canonical autophagy and the replication of enteroviruses and flaviviruses.","method":"BioID proximity labeling, mass spectrometry, siRNA knockdown, viral replication assays","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — BioID/MS interaction discovery with functional KD validation, single lab","pmids":["33277377"],"is_preprint":false},{"year":2026,"finding":"Under ER stress, TMED9 expression is transcriptionally induced by the IRE1-XBP1s pathway via a conserved UPRE-like element in its promoter. TMED9 selectively stabilizes ATF6 by preventing its ubiquitin-dependent proteasomal degradation, without affecting IRE1 or PERK signaling. TMED9 loss impairs ATF6 activation and increases sensitivity to ER stress-induced apoptosis.","method":"qRT-PCR, luciferase reporter assay, western blotting, CRISPR-Cas9 knockout, siRNA knockdown, RNA-seq, pulse-chase, ubiquitination and degradation assays, cell viability/apoptosis assays","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (reporter assay, pulse-chase, ubiquitination) in single lab; recently published with no independent replication yet","pmids":["42062868"],"is_preprint":false},{"year":2026,"finding":"PTK2/FAK inhibition triggers TMED9-mediated autophagy via enhanced ERGIC-ERES membrane contact. This non-classical autophagic flux is sensitive to TMED9 expression levels and is associated with spatial redistribution of ER exit sites (ERES). AKAP13 is a FAKi-responsive protein that undergoes dephosphorylation upon FAK inhibition and contributes to TMED9-mediated ERES-associated autophagy.","method":"High-content kinase inhibitor library screening, siRNA knockdown, live-cell imaging of ERES, co-immunoprecipitation (TMED9-ERGIC interactions), in vitro and in vivo PDAC cell viability assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — multiple methods including imaging and KD in single lab, functional in vivo confirmation, but no independent replication","pmids":["42144738"],"is_preprint":false}],"current_model":"TMED9 is a p24-family cargo receptor that cycles between the ER and Golgi as part of COPI/COPII vesicles; its cryo-EM-resolved self-oligomerization (driven by a symmetry mismatch between its coiled-coil and transmembrane domains) favors COPI recruitment and retrograde transport, enabling entrapment of misfolded protein cargos (including MUC1-fs and misfolded GPI-anchored proteins) in the early secretory pathway; TMED9 also mediates ERGIC-ERES membrane contacts via direct interaction with SEC12 to drive COPII assembly on the ERGIC and support stress-induced autophagosome biogenesis, is transcriptionally induced by IRE1-XBP1s during ER stress and stabilizes ATF6 against proteasomal degradation, and promotes pro-metastatic TGFα secretion in cancer cells; the small molecule BRD4780 binds TMED9, releases trapped misfolded cargos, and reroutes them for lysosomal degradation."},"narrative":{"mechanistic_narrative":"TMED9 is a p24-family cargo receptor of the early secretory pathway that selectively entraps misfolded protein cargos and couples ER-Golgi membrane dynamics to quality control [PMID:31348885, PMID:39303030]. Cryo-EM shows that TMED9 self-oligomerizes into octamers, dodecamers, and higher-order assemblies driven by a symmetry mismatch between its trimeric coiled-coil and tetrameric transmembrane domains; this oligomerization favors recruitment of COPI (but not COPII) coatomers to drive retrograde transport, while the luminal Golgi-dynamics domain directly engages frameshifted MUC1 cargo to explain cargo entrapment [PMID:39303030]. The same receptor functions in the RESET pathway for misfolded GPI-anchored proteins, associating specifically with misfolded (but not wild-type) GPI-APs after their release from calnexin and conveying them from the ER to the Golgi [PMID:40203033]. The small molecule BRD4780 binds TMED9 directly, releases trapped misfolded MUC1-fs cargo, and reroutes it for lysosomal degradation, with TMED9 deletion phenocopying this effect; acute BRD4780 treatment shifts TMED9 from ER to Golgi to block RESET [PMID:31348885, PMID:40203033]. Independently of cargo capture, TMED9 interacts with SEC12 at the ERGIC to establish ERGIC-ERES membrane contacts that transactivate COPII assembly on the ERGIC and support stress-induced autophagosome biogenesis, a function also engaged downstream of PTK2/FAK inhibition [PMID:34561617, PMID:42144738]. TMED9 is transcriptionally induced by the IRE1-XBP1s arm of the unfolded protein response and selectively stabilizes ATF6 by preventing its ubiquitin-dependent proteasomal degradation, linking the receptor to ER stress adaptation and survival [PMID:42062868]. In cancer, TMED9 acts downstream of TMED3 to promote pro-metastatic TGFα biogenesis and secretion and cell migration [PMID:31253868].","teleology":[{"year":2019,"claim":"Established TMED9 as a cargo receptor that entraps misfolded proteins in the early secretory pathway and as the direct target of a small-molecule that rescues this entrapment.","evidence":"Direct small-molecule binding (BRD4780), genetic deletion/knockdown phenocopy, and protein-clearance readouts across patient cells, knockin mouse kidneys, and patient kidney organoids","pmids":["31348885"],"confidence":"High","gaps":["Structural basis of misfolded-cargo recognition not defined at this stage","Whether entrapment is specific to MUC1-fs or general to misfolded cargos unresolved here"]},{"year":2021,"claim":"Revealed a cargo-independent role: TMED9 binds SEC12 at the ERGIC to nucleate ERGIC-ERES membrane contacts and COPII assembly required for stress-induced autophagosome biogenesis.","evidence":"Reciprocal Co-IP, super-resolution and electron microscopy of membrane contacts, siRNA knockdown with COPII assembly and autophagy flux assays","pmids":["34561617"],"confidence":"High","gaps":["Molecular determinants on TMED9 mediating SEC12 binding not mapped","Relationship between this COPII-promoting role and the COPI-favoring oligomeric state unresolved"]},{"year":2024,"claim":"Provided the structural mechanism for cargo entrapment: TMED9 self-oligomerizes via a coiled-coil/transmembrane symmetry mismatch, biasing coat recruitment toward COPI retrograde transport.","evidence":"Cryo-EM structure determination, domain mutagenesis, and COPI/COPII recruitment assays with luminal-domain cargo interaction","pmids":["39303030"],"confidence":"High","gaps":["How oligomeric state is regulated in cells not established","Reconciliation with TMED9's COPII-promoting ERGIC role not addressed"]},{"year":2025,"claim":"Extended TMED9's quality-control function to misfolded GPI-anchored proteins, showing selective recognition downstream of calnexin and BRD4780-dependent localization control.","evidence":"Biochemical fractionation, Co-IP, live-cell imaging, siRNA depletion, and BRD4780 treatment with ER-export readouts","pmids":["40203033"],"confidence":"High","gaps":["Structural basis for misfolded-vs-WT GPI-AP discrimination unknown","How BRD4780 shifts TMED9 from ER to Golgi mechanistically unresolved"]},{"year":2026,"claim":"Connected TMED9 to ER-stress signaling, showing it is an IRE1-XBP1s transcriptional target that in turn stabilizes ATF6 against proteasomal degradation.","evidence":"Luciferase reporter, qRT-PCR, CRISPR/siRNA loss-of-function, pulse-chase, ubiquitination/degradation and apoptosis assays","pmids":["42062868"],"confidence":"Medium","gaps":["Direct biochemical mechanism by which TMED9 protects ATF6 from ubiquitination not defined","No independent replication yet"]},{"year":2026,"claim":"Linked TMED9-driven ERGIC-ERES contacts to a druggable non-classical autophagy axis activated by PTK2/FAK inhibition in PDAC.","evidence":"Kinase-inhibitor screen, ERES live-cell imaging, Co-IP, and in vitro/in vivo PDAC viability assays implicating AKAP13","pmids":["42144738"],"confidence":"Medium","gaps":["Direct molecular link between AKAP13 dephosphorylation and TMED9 function unclear","No independent replication yet"]},{"year":null,"claim":"How TMED9's distinct activities — COPI-favoring oligomerization for cargo entrapment versus SEC12-dependent COPII promotion and ATF6 stabilization — are coordinated or switched within a single cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model integrating retrograde entrapment and forward/COPII-promoting roles","Regulation of TMED9 oligomeric state in vivo unknown","Cargo-selectivity code for misfolded proteins not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0038024","term_label":"cargo receptor activity","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,3]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[1,3]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[0,5]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2,8]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[7]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,3]}],"complexes":[],"partners":["SEC12","BPIFB3","ATF6","TMED3","CNIH4","AKAP13"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BVK6","full_name":"Transmembrane emp24 domain-containing protein 9","aliases":["GMP25","Glycoprotein 25L2","p24 family protein alpha-2","p24alpha2","p25"],"length_aa":235,"mass_kda":27.3,"function":"Appears to be involved in vesicular protein trafficking, mainly in the early secretory pathway. In COPI vesicle-mediated retrograde transport involved in the coatomer recruitment to membranes of the early secretory pathway. Increases coatomer-dependent activity of ARFGAP2. Thought to play a crucial role in the specific retention of p24 complexes in cis-Golgi membranes; specifically contributes to the coupled localization of TMED2 and TMED10 in the cis-Golgi network. May be involved in organization of intracellular membranes, such as of the ER-Golgi intermediate compartment and the Golgi apparatus. Involved in ER localization of PTPN2 isoform PTPB","subcellular_location":"Endoplasmic reticulum membrane; Golgi apparatus, cis-Golgi network membrane; Endoplasmic reticulum-Golgi intermediate compartment membrane; Golgi apparatus, trans-Golgi network membrane","url":"https://www.uniprot.org/uniprotkb/Q9BVK6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TMED9","classification":"Not Classified","n_dependent_lines":49,"n_total_lines":1208,"dependency_fraction":0.04056291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"TMED2","stoichiometry":10.0},{"gene":"CANX","stoichiometry":0.2},{"gene":"COPB2","stoichiometry":0.2},{"gene":"DDOST","stoichiometry":0.2},{"gene":"GOLGA2","stoichiometry":0.2},{"gene":"GORASP2","stoichiometry":0.2},{"gene":"MIF","stoichiometry":0.2},{"gene":"OST4","stoichiometry":0.2},{"gene":"PGRMC1","stoichiometry":0.2},{"gene":"RER1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TMED9","total_profiled":1310},"omim":[{"mim_id":"620437","title":"TRANSMEMBRANE p24 TRAFFICKING PROTEIN 3; TMED3","url":"https://www.omim.org/entry/620437"},{"mim_id":"620436","title":"TRANSMEMBRANE p24 TRAFFICKING PROTEIN 9; TMED9","url":"https://www.omim.org/entry/620436"},{"mim_id":"619990","title":"TRANSMEMBRANE p24 TRAFFICKING PROTEIN 7; TMED7","url":"https://www.omim.org/entry/619990"},{"mim_id":"619642","title":"TRANSMEMBRANE p24 TRAFFICKING PROTEIN 2; TMED2","url":"https://www.omim.org/entry/619642"},{"mim_id":"605406","title":"TRANSMEMBRANE p24 TRAFFICKING PROTEIN 10; TMED10","url":"https://www.omim.org/entry/605406"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TMED9"},"hgnc":{"alias_symbol":["HSGP25L2G","p24alpha2","p24a2"],"prev_symbol":[]},"alphafold":{"accession":"Q9BVK6","domains":[{"cath_id":"2.60.120.680","chopping":"38-149","consensus_level":"high","plddt":86.6791,"start":38,"end":149},{"cath_id":"1.20.5","chopping":"152-235","consensus_level":"medium","plddt":88.0774,"start":152,"end":235}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BVK6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BVK6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BVK6-F1-predicted_aligned_error_v6.png","plddt_mean":83.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMED9","jax_strain_url":"https://www.jax.org/strain/search?query=TMED9"},"sequence":{"accession":"Q9BVK6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BVK6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BVK6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BVK6"}},"corpus_meta":[{"pmid":"31348885","id":"PMC_31348885","title":"Small Molecule Targets TMED9 and Promotes Lysosomal Degradation to Reverse Proteinopathy.","date":"2019","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/31348885","citation_count":160,"is_preprint":false},{"pmid":"34561617","id":"PMC_34561617","title":"A new type of ERGIC-ERES membrane contact mediated by TMED9 and SEC12 is required for autophagosome biogenesis.","date":"2021","source":"Cell research","url":"https://pubmed.ncbi.nlm.nih.gov/34561617","citation_count":69,"is_preprint":false},{"pmid":"31253868","id":"PMC_31253868","title":"The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases.","date":"2019","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/31253868","citation_count":49,"is_preprint":false},{"pmid":"22114321","id":"PMC_22114321","title":"MicroRNAs 296 and 298 are imprinted and part of the GNAS/Gnas cluster and miR-296 targets IKBKE and Tmed9.","date":"2011","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/22114321","citation_count":40,"is_preprint":false},{"pmid":"36733337","id":"PMC_36733337","title":"The many hats of transmembrane emp24 domain protein TMED9 in secretory pathway homeostasis.","date":"2023","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/36733337","citation_count":19,"is_preprint":false},{"pmid":"33888099","id":"PMC_33888099","title":"Proteomics-based identification of TMED9 is linked to vascular invasion and poor prognoses in patients with hepatocellular carcinoma.","date":"2021","source":"Journal of biomedical science","url":"https://pubmed.ncbi.nlm.nih.gov/33888099","citation_count":17,"is_preprint":false},{"pmid":"33277377","id":"PMC_33277377","title":"BPIFB3 interacts with ARFGAP1 and TMED9 to regulate non-canonical autophagy and RNA virus infection.","date":"2021","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/33277377","citation_count":10,"is_preprint":false},{"pmid":"39303030","id":"PMC_39303030","title":"Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway.","date":"2024","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/39303030","citation_count":8,"is_preprint":false},{"pmid":"25438880","id":"PMC_25438880","title":"Pre-synaptic localization of the γ-secretase-inhibiting protein p24α2 in the mammalian brain.","date":"2015","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/25438880","citation_count":8,"is_preprint":false},{"pmid":"40203033","id":"PMC_40203033","title":"TMED9 coordinates the clearance of misfolded GPI-anchored proteins out of the ER and into the Golgi.","date":"2025","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/40203033","citation_count":3,"is_preprint":false},{"pmid":"40497947","id":"PMC_40497947","title":"Targeting the Cargo Receptor TMED9 as a Therapeutic Strategy Against Brain Tumors.","date":"2025","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/40497947","citation_count":1,"is_preprint":false},{"pmid":"39974996","id":"PMC_39974996","title":"TMED9 coordinates the clearance of misfolded GPI-anchored proteins out of the endoplasmic reticulum and into the Golgi.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39974996","citation_count":1,"is_preprint":false},{"pmid":"42062868","id":"PMC_42062868","title":"IRE1-XBP1driven induction of TMED9 stabilizes ATF6 during ER stress to promote cell survival.","date":"2026","source":"Cellular & molecular biology letters","url":"https://pubmed.ncbi.nlm.nih.gov/42062868","citation_count":0,"is_preprint":false},{"pmid":"42144738","id":"PMC_42144738","title":"PTK2/FAK inhibition triggers TMED9-mediated protective autophagy in pancreatic cancer cell via enhancing ERGIC-ERES contact.","date":"2026","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/42144738","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9982,"output_tokens":2620,"usd":0.034623,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9802,"output_tokens":2889,"usd":0.060617,"stage2_stop_reason":"end_turn"},"total_usd":0.09524,"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\": 2019,\n      \"finding\": \"BRD4780 binds TMED9 directly, releasing trapped misfolded MUC1-fs cargo from TMED9-containing vesicles of the early secretory pathway and re-routing it for lysosomal degradation; TMED9 deletion phenocopies this effect, establishing TMED9 as a cargo receptor that entraps misfolded proteins in the early secretory pathway.\",\n      \"method\": \"Small molecule binding assay, patient cell lines, knockin mouse kidneys, patient kidney organoids, TMED9 deletion/knockdown with protein clearance readouts\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (chemical probe, genetic deletion, organoid models), replicated across patient cells and in vivo mouse model\",\n      \"pmids\": [\"31348885\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structures reveal that TMED9 self-oligomerizes into octamers, dodecamers, and higher-order oligomers driven by an intrinsic symmetry mismatch between its trimeric coiled-coil domain and tetrameric transmembrane domain. The luminal Golgi-dynamics domain directly interacts with frameshifted MUC1 cargo. TMED9 oligomerization favors recruitment of COPI (but not COPII) coatomers, facilitating retrograde transport and explaining cargo entrapment.\",\n      \"method\": \"Cryo-electron microscopy structure determination, domain mutagenesis, COPI/COPII recruitment assays\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with functional validation of COPI/COPII recruitment and cargo interaction, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"39303030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TMED9 interacts with SEC12 at the ER-Golgi intermediate compartment (ERGIC) to establish a new ERGIC-ERES membrane contact (2–5 nm distance) that transactivates COPII assembly on the ERGIC, promotes formation of ERGIC-derived COPII vesicles, and is required for stress-induced autophagosome biogenesis.\",\n      \"method\": \"Co-immunoprecipitation, super-resolution and electron microscopy, siRNA knockdown, COPII assembly assays, autophagy flux assays\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal interaction between TMED9 and SEC12 shown with Co-IP, membrane contact quantified by EM, functional consequence confirmed by KD with autophagy readouts\",\n      \"pmids\": [\"34561617\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TMED9 plays a requisite role in the RESET pathway for quality control of misfolded GPI-anchored proteins (GPI-APs): it associates with misfolded GPI-APs (but not wild-type GPI-APs) in the ER after their release from calnexin, and conveys them to the Golgi. siRNA depletion or BRD4780 treatment blocks ER-export of misfolded GPI-APs specifically. Acute BRD4780 treatment shifts TMED9 localization from ER to Golgi cisternae, blocking RESET; removal of BRD4780 restores ER localization and RESET activity.\",\n      \"method\": \"Biochemical fractionation, co-immunoprecipitation, live-cell imaging, siRNA knockdown, chemical inhibitor (BRD4780) treatment, localization assays\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biochemical and imaging methods in single lab, specific cargo selectivity (misfolded vs. WT) demonstrated\",\n      \"pmids\": [\"40203033\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TMED9 acts downstream of TMED3 in colon cancer cells and promotes pro-metastatic behavior via regulation of TGFα biogenesis and secretion; TMED9 knockdown compromises TGFα biogenesis and impairs cell migration. TMED9 function is linked to CNIH4 (a TGFα exporter) and establishes a positive feedback loop with TGFα and GLI1 that opposes TMED3-WNT-TCF signaling.\",\n      \"method\": \"siRNA knockdown, functional rescue assays, migration/invasion assays, gene expression analysis across three colon cancer cell lines\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — epistasis and functional rescue in multiple cell lines, but no direct biochemical interaction demonstrated for the TMED9-TGFα-CNIH4 complex\",\n      \"pmids\": [\"31253868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"p24α2 (TMED9) is localized to pre-synaptic terminals in the mammalian brain and is condensed at active zone-docked synaptic vesicles, as established by immunohistochemistry, subcellular fractionation, and synaptic vesicle immunoisolation. Amyloid precursor protein and γ-secretase components co-localize at the same active zone-docked synaptic vesicles.\",\n      \"method\": \"Immunohistochemistry, subcellular fractionation, synaptic vesicle immunoisolation\",\n      \"journal\": \"Journal of neurochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — subcellular fractionation and immunoisolation establish localization, single lab with no functional loss-of-function data\",\n      \"pmids\": [\"25438880\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TMED9 interacts with BPIFB3 (identified by proximity-dependent biotinylation/BioID followed by mass spectrometry) and regulates non-canonical autophagy and the replication of enteroviruses and flaviviruses.\",\n      \"method\": \"BioID proximity labeling, mass spectrometry, siRNA knockdown, viral replication assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — BioID/MS interaction discovery with functional KD validation, single lab\",\n      \"pmids\": [\"33277377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Under ER stress, TMED9 expression is transcriptionally induced by the IRE1-XBP1s pathway via a conserved UPRE-like element in its promoter. TMED9 selectively stabilizes ATF6 by preventing its ubiquitin-dependent proteasomal degradation, without affecting IRE1 or PERK signaling. TMED9 loss impairs ATF6 activation and increases sensitivity to ER stress-induced apoptosis.\",\n      \"method\": \"qRT-PCR, luciferase reporter assay, western blotting, CRISPR-Cas9 knockout, siRNA knockdown, RNA-seq, pulse-chase, ubiquitination and degradation assays, cell viability/apoptosis assays\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (reporter assay, pulse-chase, ubiquitination) in single lab; recently published with no independent replication yet\",\n      \"pmids\": [\"42062868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PTK2/FAK inhibition triggers TMED9-mediated autophagy via enhanced ERGIC-ERES membrane contact. This non-classical autophagic flux is sensitive to TMED9 expression levels and is associated with spatial redistribution of ER exit sites (ERES). AKAP13 is a FAKi-responsive protein that undergoes dephosphorylation upon FAK inhibition and contributes to TMED9-mediated ERES-associated autophagy.\",\n      \"method\": \"High-content kinase inhibitor library screening, siRNA knockdown, live-cell imaging of ERES, co-immunoprecipitation (TMED9-ERGIC interactions), in vitro and in vivo PDAC cell viability assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — multiple methods including imaging and KD in single lab, functional in vivo confirmation, but no independent replication\",\n      \"pmids\": [\"42144738\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TMED9 is a p24-family cargo receptor that cycles between the ER and Golgi as part of COPI/COPII vesicles; its cryo-EM-resolved self-oligomerization (driven by a symmetry mismatch between its coiled-coil and transmembrane domains) favors COPI recruitment and retrograde transport, enabling entrapment of misfolded protein cargos (including MUC1-fs and misfolded GPI-anchored proteins) in the early secretory pathway; TMED9 also mediates ERGIC-ERES membrane contacts via direct interaction with SEC12 to drive COPII assembly on the ERGIC and support stress-induced autophagosome biogenesis, is transcriptionally induced by IRE1-XBP1s during ER stress and stabilizes ATF6 against proteasomal degradation, and promotes pro-metastatic TGFα secretion in cancer cells; the small molecule BRD4780 binds TMED9, releases trapped misfolded cargos, and reroutes them for lysosomal degradation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TMED9 is a p24-family cargo receptor of the early secretory pathway that selectively entraps misfolded protein cargos and couples ER-Golgi membrane dynamics to quality control [#0, #1]. Cryo-EM shows that TMED9 self-oligomerizes into octamers, dodecamers, and higher-order assemblies driven by a symmetry mismatch between its trimeric coiled-coil and tetrameric transmembrane domains; this oligomerization favors recruitment of COPI (but not COPII) coatomers to drive retrograde transport, while the luminal Golgi-dynamics domain directly engages frameshifted MUC1 cargo to explain cargo entrapment [#1]. The same receptor functions in the RESET pathway for misfolded GPI-anchored proteins, associating specifically with misfolded (but not wild-type) GPI-APs after their release from calnexin and conveying them from the ER to the Golgi [#3]. The small molecule BRD4780 binds TMED9 directly, releases trapped misfolded MUC1-fs cargo, and reroutes it for lysosomal degradation, with TMED9 deletion phenocopying this effect; acute BRD4780 treatment shifts TMED9 from ER to Golgi to block RESET [#0, #3]. Independently of cargo capture, TMED9 interacts with SEC12 at the ERGIC to establish ERGIC-ERES membrane contacts that transactivate COPII assembly on the ERGIC and support stress-induced autophagosome biogenesis, a function also engaged downstream of PTK2/FAK inhibition [#2, #8]. TMED9 is transcriptionally induced by the IRE1-XBP1s arm of the unfolded protein response and selectively stabilizes ATF6 by preventing its ubiquitin-dependent proteasomal degradation, linking the receptor to ER stress adaptation and survival [#7]. In cancer, TMED9 acts downstream of TMED3 to promote pro-metastatic TGF\\u03b1 biogenesis and secretion and cell migration [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Established TMED9 as a cargo receptor that entraps misfolded proteins in the early secretory pathway and as the direct target of a small-molecule that rescues this entrapment.\",\n      \"evidence\": \"Direct small-molecule binding (BRD4780), genetic deletion/knockdown phenocopy, and protein-clearance readouts across patient cells, knockin mouse kidneys, and patient kidney organoids\",\n      \"pmids\": [\"31348885\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of misfolded-cargo recognition not defined at this stage\", \"Whether entrapment is specific to MUC1-fs or general to misfolded cargos unresolved here\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealed a cargo-independent role: TMED9 binds SEC12 at the ERGIC to nucleate ERGIC-ERES membrane contacts and COPII assembly required for stress-induced autophagosome biogenesis.\",\n      \"evidence\": \"Reciprocal Co-IP, super-resolution and electron microscopy of membrane contacts, siRNA knockdown with COPII assembly and autophagy flux assays\",\n      \"pmids\": [\"34561617\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular determinants on TMED9 mediating SEC12 binding not mapped\", \"Relationship between this COPII-promoting role and the COPI-favoring oligomeric state unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided the structural mechanism for cargo entrapment: TMED9 self-oligomerizes via a coiled-coil/transmembrane symmetry mismatch, biasing coat recruitment toward COPI retrograde transport.\",\n      \"evidence\": \"Cryo-EM structure determination, domain mutagenesis, and COPI/COPII recruitment assays with luminal-domain cargo interaction\",\n      \"pmids\": [\"39303030\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How oligomeric state is regulated in cells not established\", \"Reconciliation with TMED9's COPII-promoting ERGIC role not addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended TMED9's quality-control function to misfolded GPI-anchored proteins, showing selective recognition downstream of calnexin and BRD4780-dependent localization control.\",\n      \"evidence\": \"Biochemical fractionation, Co-IP, live-cell imaging, siRNA depletion, and BRD4780 treatment with ER-export readouts\",\n      \"pmids\": [\"40203033\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for misfolded-vs-WT GPI-AP discrimination unknown\", \"How BRD4780 shifts TMED9 from ER to Golgi mechanistically unresolved\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Connected TMED9 to ER-stress signaling, showing it is an IRE1-XBP1s transcriptional target that in turn stabilizes ATF6 against proteasomal degradation.\",\n      \"evidence\": \"Luciferase reporter, qRT-PCR, CRISPR/siRNA loss-of-function, pulse-chase, ubiquitination/degradation and apoptosis assays\",\n      \"pmids\": [\"42062868\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical mechanism by which TMED9 protects ATF6 from ubiquitination not defined\", \"No independent replication yet\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Linked TMED9-driven ERGIC-ERES contacts to a druggable non-classical autophagy axis activated by PTK2/FAK inhibition in PDAC.\",\n      \"evidence\": \"Kinase-inhibitor screen, ERES live-cell imaging, Co-IP, and in vitro/in vivo PDAC viability assays implicating AKAP13\",\n      \"pmids\": [\"42144738\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between AKAP13 dephosphorylation and TMED9 function unclear\", \"No independent replication yet\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TMED9's distinct activities — COPI-favoring oligomerization for cargo entrapment versus SEC12-dependent COPII promotion and ATF6 stabilization — are coordinated or switched within a single cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model integrating retrograde entrapment and forward/COPII-promoting roles\", \"Regulation of TMED9 oligomeric state in vivo unknown\", \"Cargo-selectivity code for misfolded proteins not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0038024\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2, 8]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"SEC12\", \"BPIFB3\", \"ATF6\", \"TMED3\", \"CNIH4\", \"AKAP13\"],\n    \"other_free_text\": []\n  }\n}\n```","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}