{"gene":"CANX","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":1994,"finding":"Calnexin (IP90/p88), an ER membrane-bound chaperone, retards intracellular transport of peptide-deficient MHC class I heavy chain–β2-microglobulin heterodimers and free heavy chains, and impedes rapid degradation of free heavy chains, thereby retaining and protecting class I assembly intermediates in the ER.","method":"Expression of class I subunits alone or in combination with calnexin in Drosophila melanogaster cells; co-immunoprecipitation; transport assays","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reconstitution in heterologous system, transport assays, replicated across multiple class I subunit combinations","pmids":["8278813"],"is_preprint":false},{"year":1994,"finding":"Calnexin associates specifically with newly synthesized wild-type and ΔF508 mutant CFTR in the ER (co-immunoprecipitation and cosedimentation); only wild-type CFTR escapes this association and exits the ER, indicating calnexin retains misfolded or incompletely assembled CFTR.","method":"Co-immunoprecipitation, glycerol density gradient cosedimentation in human epithelial cells and recombinant CHO cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — two orthogonal biochemical methods (co-IP and cosedimentation), single lab","pmids":["7513695"],"is_preprint":false},{"year":1993,"finding":"Human IP90 (calnexin) associates transiently with many newly synthesized ER-transiting proteins; in cells lacking TCR α-chain, unassembled TCR β-chains retained in the ER remain stably associated with IP90, demonstrating its role in retaining unassembled subunits in the ER.","method":"Metabolic pulse-chase labeling, co-immunoprecipitation in T cell lines","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with pulse-chase in physiologically relevant cell models, single lab","pmids":["8486646"],"is_preprint":false},{"year":1994,"finding":"Calnexin associates rapidly with newly synthesized MHC class II α, β, and invariant (I) chains and remains associated with the assembling αβI complex until the final αβ dimer is added to form the complete nonameric structure; dissociation of calnexin parallels ER egress, indicating calnexin retains and stabilizes partially assembled class II–invariant chain complexes.","method":"Co-immunoprecipitation with pulse-chase in class II-expressing cells","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pulse-chase co-IP tracking assembly intermediates at defined time points, single lab","pmids":["8313912"],"is_preprint":false},{"year":1993,"finding":"The primary interaction site between calnexin (p88) and MHC class I heavy chains or TCR α-chain is within the transmembrane segment and flanking amino acids, not within the ER-luminal extracellular domain; GPI-anchored (non-transmembrane) variants of class I heavy chain fail to associate with p88, whereas GPI constructs engineered with the Db transmembrane region regain association.","method":"Domain deletion mutagenesis of class I heavy chains, GPI-anchor substitution hybrids, co-immunoprecipitation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — systematic mutagenesis with multiple complementary constructs, gain-of-function and loss-of-function confirmed in same study","pmids":["8349678"],"is_preprint":false},{"year":2018,"finding":"Calnexin (CNX-1, the C. elegans ortholog) is required for biogenesis of ERG-type K+ channel UNC-103: loss-of-function mutations in cnx-1 decrease UNC-103 protein level and current density; CNX-1 facilitates tetrameric assembly of UNC-103 subunits in a liposome-assisted cell-free translation system. Mammalian calnexin interacts with hERG in HEK293T cells, and calnexin deletion reduces endogenous hERG expression and current densities in SH-SY5Y cells.","method":"Forward genetic screen in C. elegans; liposome-assisted cell-free translation/assembly assay; co-immunoprecipitation in HEK293T; calnexin knockout with electrophysiology in SH-SY5Y","journal":"The Journal of general physiology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (genetic screen, in vitro reconstitution, KO + electrophysiology, co-IP), cross-organism validation","pmids":["29941431"],"is_preprint":false},{"year":2022,"finding":"CANX (calnexin) is an essential regulator of leucine-stimulated mTORC1 activation: upon leucine deprivation, CANX translocates to lysosomes, binds LAMP2, and interacts with the Ragulator complex to inhibit Ragulator's GEF activity toward RRAG GTPases. KAT7 mediates K525 crotonylation of CANX, which is required for its lysosomal translocation and mTORC1 inhibition upon leucine deprivation.","method":"Cell-free mTORC1 activation system; CANX knockout/knockdown; lysosomal fractionation; co-immunoprecipitation (CANX–LAMP2, CANX–Ragulator); GST pulldown; mass spectrometry for crotonylation; KAT7 knockout","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — cell-free reconstitution, multiple co-IPs, lysosomal fractionation, PTM identified with writer (KAT7), functional rescue experiments in same study","pmids":["35266843"],"is_preprint":false},{"year":2021,"finding":"miR-148a-3p directly targets CANX mRNA (validated by luciferase assay), reducing CANX protein levels and consequently decreasing MHC-I surface expression, thereby impairing CD8+ T cell-mediated killing of colorectal cancer cells; inhibition of miR-148a-3p restores CANX expression and MHC-I surface levels.","method":"miRNA target prediction, luciferase reporter assay, CANX knockdown/rescue, in vitro CD8+ T cell cytotoxicity assay, in vivo tumor models","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase validation of miRNA targeting, functional rescue, single lab","pmids":["34324740"],"is_preprint":false},{"year":2025,"finding":"CANX (calnexin) is a novel interaction partner of autophagy-initiating kinase ULK1 and is required for ULK1 recruitment to the ER under basal and starved conditions; loss of CANX inactivates ULK1 and inhibits autophagy flux; overexpression of CANX enhances autophagy flux and improves cognitive function in APP-PSEN1 AD mice, but a CANX variant lacking the ULK1 interaction domain does not.","method":"Co-immunoprecipitation, proximity ligation assay, bimolecular fluorescence complementation, CANX knockout in hippocampal neurons, LC3/autophagy flux assays, Morris water maze behavioral test, domain-deletion rescue experiments","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal interaction methods (co-IP, PLA, BiFC), KO with autophagy flux readout, domain-deletion rescue, in vivo behavioral validation","pmids":["39813987"],"is_preprint":false},{"year":2025,"finding":"CANX forms a misfolded-protein segregation complex with the ER-phagy receptor FAM134B and LC3 at ER–endolysosome membrane contact sites (involving the VAPA:ORP1L:RAB7 complex) to drive ERLAD (ER-to-lysosome-associated degradation) of ATZ (Z-variant alpha1-antitrypsin) polymers, facilitating SNARE-regulated membrane fusion events (STX17 and VAMP8) for ATZ delivery to degradative endolysosomes.","method":"Fluorescence microscopy of membrane contact sites, proximity assays, investigation of ATZ intracellular fate in cells with manipulated CANX, FAM134B, VAPA, ORP1L, RAB7","journal":"Autophagy reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multi-component complex characterization, functional degradation assay, single study","pmids":["41179805"],"is_preprint":false},{"year":2025,"finding":"CBL is an E3 ubiquitin ligase for CANX that induces CANX ubiquitination and degradation; HBV core protein (HBC) stabilizes CANX by disrupting the CANX–CBL interaction. CANX in turn suppresses IRF7 gene transcription via HDAC3, which is recruited to the IRF7 promoter through CANX–HDAC3 interaction enhanced by HBC.","method":"Co-immunoprecipitation (CANX–CBL, CANX–HDAC3), ubiquitination assays, chromatin-associated assays for HDAC3 at IRF7 promoter, CANX knockdown/overexpression in tumor cells in vitro and in vivo","journal":"Acta pharmacologica Sinica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP for E3 ligase and transcriptional co-repressor interactions, ubiquitination assay, single lab","pmids":["40514420"],"is_preprint":false},{"year":2026,"finding":"TRIM27 acts as an E3 ubiquitin ligase that ubiquitinates CANX, promoting its degradation and activating PI3K/AKT signaling in prostate cancer cells.","method":"Co-immunoprecipitation, ubiquitination assays, TRIM27 knockdown/overexpression with CANX protein level and PI3K/AKT pathway readouts in vitro","journal":"Functional & integrative genomics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, co-IP and ubiquitination assay without mutagenesis or reconstitution, limited mechanistic detail in abstract","pmids":["41557161"],"is_preprint":false},{"year":2023,"finding":"PON2 interacts with CANX (confirmed by co-immunoprecipitation) and PON2 overexpression inhibits CANX/NOX4 signaling, reducing oxidative stress, inflammation, hypertrophy, and apoptosis in Ang II-stimulated cardiomyocytes.","method":"Co-immunoprecipitation, PON2 overexpression with ROS/oxidative stress assays, ELISA, Western blot in AC16 cells","journal":"Immunity, inflammation and disease","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single co-IP method, limited mechanistic resolution of CANX role in the pathway","pmids":["36840500"],"is_preprint":false},{"year":2022,"finding":"CANX (calnexin) overexpression in colorectal cancer cells upregulates surface MHC-I expression; CANX knockdown downregulates MHC-I, and CANX overexpression enhances CD8+ T cell killing and promotes IFN-γ and TNF-α secretion.","method":"Western blot, lentiviral overexpression, siRNA knockdown, CD8+ T cell co-culture cytotoxicity assay, ELISA","journal":"Chinese journal of cellular and molecular immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function and gain-of-function with defined functional readouts (MHC-I surface level, T cell killing), single lab","pmids":["35356876"],"is_preprint":false}],"current_model":"Calnexin (CANX/CNX/IP90) is an ER transmembrane lectin-chaperone that retains and stabilizes incompletely assembled or misfolded membrane proteins (MHC class I and II, CFTR, TCR subunits, hERG/ERG-type K+ channels) in the ER via preferential interaction with their transmembrane segments; beyond classical ER quality control, calnexin undergoes KAT7-mediated K525 crotonylation that drives its lysosomal translocation to inhibit Ragulator-RRAG GTPase activity and suppress leucine-stimulated mTORC1, interacts with ULK1 at the ER to support autophagy initiation, and forms a complex with FAM134B and LC3 at ER–endolysosome membrane contact sites to mediate ERLAD of misfolded polymers; its stability is regulated by CBL- and TRIM27-mediated ubiquitination, and its transcriptional output includes suppression of IRF7 via HDAC3 recruitment."},"narrative":{"mechanistic_narrative":"Calnexin (CANX/IP90/p88) is an ER transmembrane chaperone that mediates quality control of newly synthesized membrane proteins by retaining and stabilizing incompletely assembled or misfolded intermediates in the ER until proper assembly is achieved [PMID:8278813, PMID:8486646]. It associates transiently with a broad range of ER-transiting proteins and holds onto unassembled subunits—peptide-deficient MHC class I heavy chain–β2-microglobulin heterodimers and free heavy chains, unassembled TCR β-chains, and partially assembled MHC class II α/β/invariant-chain complexes—releasing them only upon completion of assembly and ER egress [PMID:8278813, PMID:8486646, PMID:8313912]. This recognition is directed primarily at the transmembrane segment and flanking residues of client proteins rather than their luminal domains, as GPI-anchored class I variants fail to bind calnexin unless engineered to carry a transmembrane region [PMID:8349678]. Through this activity calnexin supports biogenesis and surface delivery of clients including ΔF508-sensitive CFTR [PMID:7513695], ERG/hERG-type K+ channels where it facilitates tetrameric assembly [PMID:29941431], and cell-surface MHC-I, with calnexin levels setting MHC-I display and consequent CD8+ T-cell-mediated cytotoxicity [PMID:34324740, PMID:35356876]. Beyond classical ER quality control, calnexin acts in protein-degradation and autophagy pathways: it partners with the ER-phagy receptor FAM134B and LC3 at ER–endolysosome membrane contact sites to drive ERLAD of misfolded alpha-1-antitrypsin (ATZ) polymers [PMID:41179805], serves as an interaction partner required for ULK1 recruitment to the ER and for autophagy initiation [PMID:39813987], and—following KAT7-mediated K525 crotonylation—translocates to lysosomes where it binds LAMP2 and inhibits Ragulator GEF activity toward RRAG GTPases to suppress leucine-stimulated mTORC1 [PMID:35266843]. Calnexin abundance is controlled by ubiquitin-mediated degradation via the E3 ligases CBL and TRIM27 [PMID:40514420, PMID:41557161], and it can repress IRF7 transcription by recruiting HDAC3 to the IRF7 promoter [PMID:40514420].","teleology":[{"year":1993,"claim":"Established calnexin as a general ER retention chaperone by showing it transiently binds many nascent ER-transiting proteins and stably holds unassembled subunits when assembly partners are absent.","evidence":"Pulse-chase metabolic labeling and co-immunoprecipitation of unassembled TCR β-chains with IP90 in T cell lines","pmids":["8486646"],"confidence":"Medium","gaps":["Did not define the structural basis of client recognition","Single-lab co-IP without reconstitution"]},{"year":1993,"claim":"Resolved how calnexin recognizes clients, showing the interaction is mediated by the transmembrane segment and flanking residues rather than the luminal domain.","evidence":"Domain-deletion mutagenesis, GPI-anchor substitution hybrids, and co-IP with class I heavy chains and TCR α-chain","pmids":["8349678"],"confidence":"High","gaps":["Does not address calnexin's lectin/glycan-dependent recognition mode","Mapped on a limited set of clients"]},{"year":1994,"claim":"Demonstrated a functional consequence of calnexin binding—retention and protection of MHC class I assembly intermediates and partially assembled class II complexes, slowing transport and impeding degradation until assembly completes.","evidence":"Heterologous reconstitution in Drosophila cells with transport assays, and pulse-chase co-IP tracking class II assembly intermediates","pmids":["8278813","8313912"],"confidence":"High","gaps":["Mechanism of release upon completed assembly not defined","Quantitative contribution to degradation kinetics not isolated"]},{"year":1994,"claim":"Extended calnexin's quality-control role to a disease-relevant client, showing it discriminates wild-type from misfolded CFTR by retaining the misfolded form in the ER.","evidence":"Co-immunoprecipitation and glycerol density gradient cosedimentation of nascent CFTR in epithelial and CHO cells","pmids":["7513695"],"confidence":"High","gaps":["Did not establish whether retention promotes folding or commits CFTR to degradation"]},{"year":2018,"claim":"Showed calnexin actively assists multimeric channel assembly, not merely retention, by facilitating tetramerization of ERG-type K+ channels and being required for hERG surface expression.","evidence":"C. elegans forward genetic screen, liposome-assisted cell-free assembly assay, calnexin KO with electrophysiology, and co-IP across species","pmids":["29941431"],"confidence":"High","gaps":["Structural basis of assembly assistance not resolved","Whether assembly chaperoning generalizes to other tetrameric channels unknown"]},{"year":2021,"claim":"Identified upstream regulation of calnexin by miR-148a-3p, linking calnexin abundance to MHC-I surface levels and antitumor immunity.","evidence":"Luciferase reporter validation of miRNA targeting, CANX knockdown/rescue, and CD8+ T cell cytotoxicity assays with in vivo tumor models","pmids":["34324740"],"confidence":"Medium","gaps":["Does not establish the molecular step at which calnexin controls MHC-I trafficking","Single-lab"]},{"year":2022,"claim":"Revealed a non-canonical calnexin function as a negative regulator of nutrient signaling, showing crotonylation-driven lysosomal translocation inhibits Ragulator GEF activity to suppress leucine-stimulated mTORC1.","evidence":"Cell-free mTORC1 reconstitution, lysosomal fractionation, CANX–LAMP2 and CANX–Ragulator co-IPs, mass spectrometry of K525 crotonylation, and KAT7 KO with functional rescue","pmids":["35266843"],"confidence":"High","gaps":["How an ER membrane protein relocates to lysosomes mechanistically unresolved","Crosstalk with calnexin's ER chaperone pool unclear"]},{"year":2022,"claim":"Provided gain- and loss-of-function evidence that calnexin sets MHC-I surface levels and tunes CD8+ T-cell killing in colorectal cancer.","evidence":"Lentiviral overexpression and siRNA knockdown with MHC-I Western blot, CD8+ T cell co-culture cytotoxicity, and cytokine ELISA","pmids":["35356876"],"confidence":"Medium","gaps":["Mechanistic step controlling surface MHC-I not pinpointed","Single-lab"]},{"year":2025,"claim":"Placed calnexin upstream of autophagy initiation by identifying it as a ULK1 partner required for ULK1 recruitment to the ER, with in vivo cognitive consequences in an AD model.","evidence":"Co-IP, proximity ligation, BiFC, CANX KO in hippocampal neurons with LC3/flux assays, domain-deletion rescue, and Morris water maze testing","pmids":["39813987"],"confidence":"High","gaps":["Structural ULK1-binding determinant within calnexin not mapped","Relationship to calnexin's chaperone function unknown"]},{"year":2025,"claim":"Connected calnexin to ER-to-lysosome degradation by showing it forms a segregation complex with FAM134B and LC3 at ER–endolysosome contact sites to deliver misfolded ATZ polymers for degradation.","evidence":"Fluorescence microscopy of membrane contact sites, proximity assays, and ATZ fate tracking with manipulation of CANX, FAM134B, VAPA, ORP1L, RAB7","pmids":["41179805"],"confidence":"Medium","gaps":["Direct binding interfaces within the complex not defined","Single study"]},{"year":2026,"claim":"Characterized post-translational control of calnexin stability, identifying CBL and TRIM27 as E3 ligases that ubiquitinate and degrade calnexin, and a transcriptional repressor role via HDAC3 recruitment to IRF7.","evidence":"Co-IP, ubiquitination assays, chromatin-associated HDAC3 assays at the IRF7 promoter, and CANX knockdown/overexpression in tumor cells with PI3K/AKT readouts","pmids":["40514420","41557161"],"confidence":"Medium","gaps":["Ubiquitination sites not mapped","TRIM27 link rests on co-IP/ubiquitination without mutagenesis or reconstitution","How an ER chaperone reaches gene promoters mechanistically unresolved"]},{"year":null,"claim":"How calnexin partitions between its canonical ER chaperone pool and its non-canonical roles at lysosomes, ER-phagy contact sites, and gene promoters—and how post-translational marks like K525 crotonylation switch between these functions—remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model linking client recognition to relocalization","Quantitative flux of calnexin between compartments unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[0,2,3,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[6]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[10]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1,2,8]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[6,9]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1,5]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,2,3,5]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,7,13]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[8,9]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6,11]}],"complexes":["CANX–FAM134B–LC3 ER-phagy segregation complex"],"partners":["LAMP2","RRAGA","ULK1","FAM134B","MAP1LC3B","CBL","HDAC3","TRIM27"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P27824","full_name":"Calnexin","aliases":["IP90","Major histocompatibility complex class I antigen-binding protein p88","p90"],"length_aa":592,"mass_kda":67.6,"function":"Calcium-binding protein that interacts with newly synthesized monoglucosylated glycoproteins in the endoplasmic reticulum. It may act in assisting protein assembly and/or in the retention within the ER of unassembled protein subunits. It seems to play a major role in the quality control apparatus of the ER by the retention of incorrectly folded proteins. Associated with partial T-cell antigen receptor complexes that escape the ER of immature thymocytes, it may function as a signaling complex regulating thymocyte maturation. Additionally it may play a role in receptor-mediated endocytosis at the synapse","subcellular_location":"Endoplasmic reticulum membrane; Mitochondrion membrane; Melanosome membrane","url":"https://www.uniprot.org/uniprotkb/P27824/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CANX","classification":"Not Classified","n_dependent_lines":8,"n_total_lines":1208,"dependency_fraction":0.006622516556291391},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000127022","cell_line_id":"CID000149","localizations":[{"compartment":"er","grade":3}],"interactors":[{"gene":"DAD1","stoichiometry":10.0},{"gene":"RPN1","stoichiometry":4.0},{"gene":"EMD","stoichiometry":4.0},{"gene":"SSR4","stoichiometry":4.0},{"gene":"HSPA5","stoichiometry":4.0},{"gene":"HM13","stoichiometry":4.0},{"gene":"PPT1","stoichiometry":4.0},{"gene":"TMX1","stoichiometry":4.0},{"gene":"VMA21","stoichiometry":4.0},{"gene":"ANKRD46","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000149","total_profiled":1310},"omim":[{"mim_id":"620096","title":"RING FINGER PROTEIN 185; RNF185","url":"https://www.omim.org/entry/620096"},{"mim_id":"618203","title":"TRANSMEMBRANE AND TETRATRICOPEPTIDE REPEAT DOMAINS-CONTAINING PROTEIN 4; TMTC4","url":"https://www.omim.org/entry/618203"},{"mim_id":"617674","title":"STRESS-ASSOCIATED ENDOPLASMIC RETICULUM PROTEIN 1; SERP1","url":"https://www.omim.org/entry/617674"},{"mim_id":"616766","title":"THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN 4; TMX4","url":"https://www.omim.org/entry/616766"},{"mim_id":"616715","title":"THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN 2; TMX2","url":"https://www.omim.org/entry/616715"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Endoplasmic reticulum","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CANX"},"hgnc":{"alias_symbol":["CNX","IP90","P90"],"prev_symbol":[]},"alphafold":{"accession":"P27824","domains":[{"cath_id":"2.60.120.200","chopping":"70-273_413-454","consensus_level":"high","plddt":90.5958,"start":70,"end":454},{"cath_id":"-","chopping":"319-371","consensus_level":"medium","plddt":88.2226,"start":319,"end":371}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P27824","model_url":"https://alphafold.ebi.ac.uk/files/AF-P27824-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P27824-F1-predicted_aligned_error_v6.png","plddt_mean":76.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CANX","jax_strain_url":"https://www.jax.org/strain/search?query=CANX"},"sequence":{"accession":"P27824","fasta_url":"https://rest.uniprot.org/uniprotkb/P27824.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P27824/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P27824"}},"corpus_meta":[{"pmid":"8278813","id":"PMC_8278813","title":"Regulation of MHC class I transport by the molecular chaperone, calnexin (p88, IP90).","date":"1994","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8278813","citation_count":297,"is_preprint":false},{"pmid":"7513695","id":"PMC_7513695","title":"Participation of the endoplasmic reticulum chaperone calnexin (p88, IP90) in the biogenesis of the cystic fibrosis transmembrane conductance regulator.","date":"1994","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7513695","citation_count":287,"is_preprint":false},{"pmid":"8486646","id":"PMC_8486646","title":"Interaction with newly synthesized and retained proteins in the endoplasmic reticulum suggests a chaperone function for human integral membrane protein IP90 (calnexin).","date":"1993","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8486646","citation_count":186,"is_preprint":false},{"pmid":"8313912","id":"PMC_8313912","title":"A role for calnexin (IP90) in the assembly of class II MHC molecules.","date":"1994","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/8313912","citation_count":134,"is_preprint":false},{"pmid":"8349678","id":"PMC_8349678","title":"Identification of the region on the class I histocompatibility molecule that interacts with the molecular chaperone, p88 (calnexin, IP90).","date":"1993","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8349678","citation_count":72,"is_preprint":false},{"pmid":"18203437","id":"PMC_18203437","title":"Thermal ablation therapeutics based on CN(x) multi-walled nanotubes.","date":"2007","source":"International journal of nanomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/18203437","citation_count":70,"is_preprint":false},{"pmid":"34324740","id":"PMC_34324740","title":"miR-148a-3p silences the CANX/MHC-I pathway and impairs CD8+ T cell-mediated immune attack in colorectal cancer.","date":"2021","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/34324740","citation_count":48,"is_preprint":false},{"pmid":"796678","id":"PMC_796678","title":"Formation of NADPH-nitrate reductase activity in vitro from Aspergillus nidulans niaD and cnx mutants.","date":"1976","source":"Molecular & general genetics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/796678","citation_count":39,"is_preprint":false},{"pmid":"12603744","id":"PMC_12603744","title":"Characterization of the vls antigenic variation loci of the Lyme disease spirochaetes Borrelia garinii Ip90 and Borrelia afzelii ACAI.","date":"2003","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/12603744","citation_count":32,"is_preprint":false},{"pmid":"36341997","id":"PMC_36341997","title":"ENT1 blockade by CNX-774 overcomes resistance to DHODH inhibition in pancreatic cancer.","date":"2022","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/36341997","citation_count":24,"is_preprint":false},{"pmid":"23692921","id":"PMC_23692921","title":"Treatment with CNX-011-67, a novel GPR40 agonist, delays onset and progression of diabetes and improves beta cell preservation and function in male ZDF rats.","date":"2013","source":"BMC pharmacology & toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/23692921","citation_count":23,"is_preprint":false},{"pmid":"35266843","id":"PMC_35266843","title":"KAT7-mediated CANX (calnexin) crotonylation regulates leucine-stimulated MTORC1 activity.","date":"2022","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/35266843","citation_count":20,"is_preprint":false},{"pmid":"24666736","id":"PMC_24666736","title":"CNX-011-67, a novel GPR40 agonist, enhances glucose responsiveness, insulin secretion and islet insulin content in n-STZ rats and in islets from type 2 diabetic patients.","date":"2014","source":"BMC pharmacology & toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/24666736","citation_count":19,"is_preprint":false},{"pmid":"25098735","id":"PMC_25098735","title":"A novel 11β-hydroxysteroid dehydrogenase type1 inhibitor CNX-010-49 improves hyperglycemia, lipid profile and reduces body weight in diet induced obese C57B6/J mice with a potential to provide cardio protective benefits.","date":"2014","source":"BMC pharmacology & toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/25098735","citation_count":16,"is_preprint":false},{"pmid":"24460834","id":"PMC_24460834","title":"CNX-012-570, a direct AMPK activator provides strong glycemic and lipid control along with significant reduction in body weight; studies from both diet-induced obese mice and db/db mice models.","date":"2014","source":"Cardiovascular diabetology","url":"https://pubmed.ncbi.nlm.nih.gov/24460834","citation_count":13,"is_preprint":false},{"pmid":"29941431","id":"PMC_29941431","title":"A forward genetic screen identifies chaperone CNX-1 as a conserved biogenesis regulator of ERG K+ channels.","date":"2018","source":"The Journal of general physiology","url":"https://pubmed.ncbi.nlm.nih.gov/29941431","citation_count":11,"is_preprint":false},{"pmid":"29197784","id":"PMC_29197784","title":"Simulated photoperiod influences testicular activity in quail via modulating local GnRHR-GnIHR, GH-R, Cnx-43 and 14-3-3.","date":"2017","source":"Journal of photochemistry and photobiology. B, Biology","url":"https://pubmed.ncbi.nlm.nih.gov/29197784","citation_count":11,"is_preprint":false},{"pmid":"25143786","id":"PMC_25143786","title":"CNX-013-B2, a unique pan tissue acting rexinoid, modulates several nuclear receptors and controls multiple risk factors of the metabolic syndrome without risk of hypertriglyceridemia, hepatomegaly and body weight gain in animal models.","date":"2014","source":"Diabetology & metabolic syndrome","url":"https://pubmed.ncbi.nlm.nih.gov/25143786","citation_count":10,"is_preprint":false},{"pmid":"330163","id":"PMC_330163","title":"The genetic control of molybdoflavoproteins in Aspergillus nidulans. A xanthine dehydrogenase I half-molecule in cnx- mutant strains of Aspergillus nidulans.","date":"1977","source":"European journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/330163","citation_count":10,"is_preprint":false},{"pmid":"36840500","id":"PMC_36840500","title":"PON2 ameliorates Ang II-induced cardiomyocyte injury by targeting the CANX/NOX4 signaling pathway.","date":"2023","source":"Immunity, inflammation and disease","url":"https://pubmed.ncbi.nlm.nih.gov/36840500","citation_count":6,"is_preprint":false},{"pmid":"37023515","id":"PMC_37023515","title":"Interface engineering Ni/Ni12P5@CNx Mott-Schottky heterojunction tailoring electrocatalytic pathways for zinc-air battery.","date":"2023","source":"Journal of colloid and interface science","url":"https://pubmed.ncbi.nlm.nih.gov/37023515","citation_count":6,"is_preprint":false},{"pmid":"39161338","id":"PMC_39161338","title":"Dihydroartemisinin inhibits ATP6 activity, reduces energy metabolism of hepatocellular carcinoma cells, promotes apoptosis and inhibits metastasis via CANX.","date":"2024","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/39161338","citation_count":4,"is_preprint":false},{"pmid":"25186493","id":"PMC_25186493","title":"A novel GPR40 agonist, CNX-011-67, suppresses glucagon secretion in pancreatic islets under chronic glucolipotoxic conditions in vitro.","date":"2014","source":"BMC research notes","url":"https://pubmed.ncbi.nlm.nih.gov/25186493","citation_count":4,"is_preprint":false},{"pmid":"39813987","id":"PMC_39813987","title":"The ER protein CANX (calnexin)-mediated autophagy protects against alzheimer disease.","date":"2025","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/39813987","citation_count":3,"is_preprint":false},{"pmid":"38968858","id":"PMC_38968858","title":"A Fe2O3/CNx cascade nanoreactor with dual-enzyme-mimetic activities for cancer hypoxia relief to amplify chemo/photodynamic therapy.","date":"2024","source":"Colloids and surfaces. B, Biointerfaces","url":"https://pubmed.ncbi.nlm.nih.gov/38968858","citation_count":3,"is_preprint":false},{"pmid":"40514420","id":"PMC_40514420","title":"Hepatitis B virus core protein promotes liver cancer progression by stabilizing CANX and suppressing IRF7 transcription.","date":"2025","source":"Acta pharmacologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/40514420","citation_count":1,"is_preprint":false},{"pmid":"40655469","id":"PMC_40655469","title":"Hsa_circ_0007991 Promotes Immune Evasion in Hepatocellular Carcinoma via Regulation of the miR-505-3p/CANX Axis.","date":"2025","source":"Journal of hepatocellular carcinoma","url":"https://pubmed.ncbi.nlm.nih.gov/40655469","citation_count":1,"is_preprint":false},{"pmid":"35356876","id":"PMC_35356876","title":"[Calnexin (CNX) enhances the killing effect of CD8+ T cells on colorectal cancer cells by promoting MHC I expression].","date":"2022","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35356876","citation_count":1,"is_preprint":false},{"pmid":"40619124","id":"PMC_40619124","title":"Single-cycle Rift Valley fever virus particles from stable replicon cells enable discovery of antiviral CNX-1351 for multiple RNA viruses.","date":"2025","source":"Virologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/40619124","citation_count":0,"is_preprint":false},{"pmid":"41557161","id":"PMC_41557161","title":"MYC-driven TRIM27 upregulation promotes prostate cancer progression by enhancing CANX ubiquitination and activating PI3K/AKT signaling.","date":"2026","source":"Functional & integrative genomics","url":"https://pubmed.ncbi.nlm.nih.gov/41557161","citation_count":0,"is_preprint":false},{"pmid":"41179805","id":"PMC_41179805","title":"CNX:FAM134B-driven ERLAD of ATZ polymers proceeds via enhanced formation of VAPA:ORP1L:RAB7 contact sites between ER and endolysosomes.","date":"2025","source":"Autophagy reports","url":"https://pubmed.ncbi.nlm.nih.gov/41179805","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":18591,"output_tokens":3783,"usd":0.056259,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11417,"output_tokens":4105,"usd":0.079855,"stage2_stop_reason":"end_turn"},"total_usd":0.136114,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1994,\n      \"finding\": \"Calnexin (IP90/p88), an ER membrane-bound chaperone, retards intracellular transport of peptide-deficient MHC class I heavy chain–β2-microglobulin heterodimers and free heavy chains, and impedes rapid degradation of free heavy chains, thereby retaining and protecting class I assembly intermediates in the ER.\",\n      \"method\": \"Expression of class I subunits alone or in combination with calnexin in Drosophila melanogaster cells; co-immunoprecipitation; transport assays\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reconstitution in heterologous system, transport assays, replicated across multiple class I subunit combinations\",\n      \"pmids\": [\"8278813\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Calnexin associates specifically with newly synthesized wild-type and ΔF508 mutant CFTR in the ER (co-immunoprecipitation and cosedimentation); only wild-type CFTR escapes this association and exits the ER, indicating calnexin retains misfolded or incompletely assembled CFTR.\",\n      \"method\": \"Co-immunoprecipitation, glycerol density gradient cosedimentation in human epithelial cells and recombinant CHO cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal biochemical methods (co-IP and cosedimentation), single lab\",\n      \"pmids\": [\"7513695\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Human IP90 (calnexin) associates transiently with many newly synthesized ER-transiting proteins; in cells lacking TCR α-chain, unassembled TCR β-chains retained in the ER remain stably associated with IP90, demonstrating its role in retaining unassembled subunits in the ER.\",\n      \"method\": \"Metabolic pulse-chase labeling, co-immunoprecipitation in T cell lines\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with pulse-chase in physiologically relevant cell models, single lab\",\n      \"pmids\": [\"8486646\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Calnexin associates rapidly with newly synthesized MHC class II α, β, and invariant (I) chains and remains associated with the assembling αβI complex until the final αβ dimer is added to form the complete nonameric structure; dissociation of calnexin parallels ER egress, indicating calnexin retains and stabilizes partially assembled class II–invariant chain complexes.\",\n      \"method\": \"Co-immunoprecipitation with pulse-chase in class II-expressing cells\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pulse-chase co-IP tracking assembly intermediates at defined time points, single lab\",\n      \"pmids\": [\"8313912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"The primary interaction site between calnexin (p88) and MHC class I heavy chains or TCR α-chain is within the transmembrane segment and flanking amino acids, not within the ER-luminal extracellular domain; GPI-anchored (non-transmembrane) variants of class I heavy chain fail to associate with p88, whereas GPI constructs engineered with the Db transmembrane region regain association.\",\n      \"method\": \"Domain deletion mutagenesis of class I heavy chains, GPI-anchor substitution hybrids, co-immunoprecipitation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — systematic mutagenesis with multiple complementary constructs, gain-of-function and loss-of-function confirmed in same study\",\n      \"pmids\": [\"8349678\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Calnexin (CNX-1, the C. elegans ortholog) is required for biogenesis of ERG-type K+ channel UNC-103: loss-of-function mutations in cnx-1 decrease UNC-103 protein level and current density; CNX-1 facilitates tetrameric assembly of UNC-103 subunits in a liposome-assisted cell-free translation system. Mammalian calnexin interacts with hERG in HEK293T cells, and calnexin deletion reduces endogenous hERG expression and current densities in SH-SY5Y cells.\",\n      \"method\": \"Forward genetic screen in C. elegans; liposome-assisted cell-free translation/assembly assay; co-immunoprecipitation in HEK293T; calnexin knockout with electrophysiology in SH-SY5Y\",\n      \"journal\": \"The Journal of general physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (genetic screen, in vitro reconstitution, KO + electrophysiology, co-IP), cross-organism validation\",\n      \"pmids\": [\"29941431\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CANX (calnexin) is an essential regulator of leucine-stimulated mTORC1 activation: upon leucine deprivation, CANX translocates to lysosomes, binds LAMP2, and interacts with the Ragulator complex to inhibit Ragulator's GEF activity toward RRAG GTPases. KAT7 mediates K525 crotonylation of CANX, which is required for its lysosomal translocation and mTORC1 inhibition upon leucine deprivation.\",\n      \"method\": \"Cell-free mTORC1 activation system; CANX knockout/knockdown; lysosomal fractionation; co-immunoprecipitation (CANX–LAMP2, CANX–Ragulator); GST pulldown; mass spectrometry for crotonylation; KAT7 knockout\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — cell-free reconstitution, multiple co-IPs, lysosomal fractionation, PTM identified with writer (KAT7), functional rescue experiments in same study\",\n      \"pmids\": [\"35266843\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"miR-148a-3p directly targets CANX mRNA (validated by luciferase assay), reducing CANX protein levels and consequently decreasing MHC-I surface expression, thereby impairing CD8+ T cell-mediated killing of colorectal cancer cells; inhibition of miR-148a-3p restores CANX expression and MHC-I surface levels.\",\n      \"method\": \"miRNA target prediction, luciferase reporter assay, CANX knockdown/rescue, in vitro CD8+ T cell cytotoxicity assay, in vivo tumor models\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase validation of miRNA targeting, functional rescue, single lab\",\n      \"pmids\": [\"34324740\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CANX (calnexin) is a novel interaction partner of autophagy-initiating kinase ULK1 and is required for ULK1 recruitment to the ER under basal and starved conditions; loss of CANX inactivates ULK1 and inhibits autophagy flux; overexpression of CANX enhances autophagy flux and improves cognitive function in APP-PSEN1 AD mice, but a CANX variant lacking the ULK1 interaction domain does not.\",\n      \"method\": \"Co-immunoprecipitation, proximity ligation assay, bimolecular fluorescence complementation, CANX knockout in hippocampal neurons, LC3/autophagy flux assays, Morris water maze behavioral test, domain-deletion rescue experiments\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal interaction methods (co-IP, PLA, BiFC), KO with autophagy flux readout, domain-deletion rescue, in vivo behavioral validation\",\n      \"pmids\": [\"39813987\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CANX forms a misfolded-protein segregation complex with the ER-phagy receptor FAM134B and LC3 at ER–endolysosome membrane contact sites (involving the VAPA:ORP1L:RAB7 complex) to drive ERLAD (ER-to-lysosome-associated degradation) of ATZ (Z-variant alpha1-antitrypsin) polymers, facilitating SNARE-regulated membrane fusion events (STX17 and VAMP8) for ATZ delivery to degradative endolysosomes.\",\n      \"method\": \"Fluorescence microscopy of membrane contact sites, proximity assays, investigation of ATZ intracellular fate in cells with manipulated CANX, FAM134B, VAPA, ORP1L, RAB7\",\n      \"journal\": \"Autophagy reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multi-component complex characterization, functional degradation assay, single study\",\n      \"pmids\": [\"41179805\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CBL is an E3 ubiquitin ligase for CANX that induces CANX ubiquitination and degradation; HBV core protein (HBC) stabilizes CANX by disrupting the CANX–CBL interaction. CANX in turn suppresses IRF7 gene transcription via HDAC3, which is recruited to the IRF7 promoter through CANX–HDAC3 interaction enhanced by HBC.\",\n      \"method\": \"Co-immunoprecipitation (CANX–CBL, CANX–HDAC3), ubiquitination assays, chromatin-associated assays for HDAC3 at IRF7 promoter, CANX knockdown/overexpression in tumor cells in vitro and in vivo\",\n      \"journal\": \"Acta pharmacologica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP for E3 ligase and transcriptional co-repressor interactions, ubiquitination assay, single lab\",\n      \"pmids\": [\"40514420\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TRIM27 acts as an E3 ubiquitin ligase that ubiquitinates CANX, promoting its degradation and activating PI3K/AKT signaling in prostate cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, TRIM27 knockdown/overexpression with CANX protein level and PI3K/AKT pathway readouts in vitro\",\n      \"journal\": \"Functional & integrative genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, co-IP and ubiquitination assay without mutagenesis or reconstitution, limited mechanistic detail in abstract\",\n      \"pmids\": [\"41557161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PON2 interacts with CANX (confirmed by co-immunoprecipitation) and PON2 overexpression inhibits CANX/NOX4 signaling, reducing oxidative stress, inflammation, hypertrophy, and apoptosis in Ang II-stimulated cardiomyocytes.\",\n      \"method\": \"Co-immunoprecipitation, PON2 overexpression with ROS/oxidative stress assays, ELISA, Western blot in AC16 cells\",\n      \"journal\": \"Immunity, inflammation and disease\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single co-IP method, limited mechanistic resolution of CANX role in the pathway\",\n      \"pmids\": [\"36840500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CANX (calnexin) overexpression in colorectal cancer cells upregulates surface MHC-I expression; CANX knockdown downregulates MHC-I, and CANX overexpression enhances CD8+ T cell killing and promotes IFN-γ and TNF-α secretion.\",\n      \"method\": \"Western blot, lentiviral overexpression, siRNA knockdown, CD8+ T cell co-culture cytotoxicity assay, ELISA\",\n      \"journal\": \"Chinese journal of cellular and molecular immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function and gain-of-function with defined functional readouts (MHC-I surface level, T cell killing), single lab\",\n      \"pmids\": [\"35356876\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"Calnexin (CANX/CNX/IP90) is an ER transmembrane lectin-chaperone that retains and stabilizes incompletely assembled or misfolded membrane proteins (MHC class I and II, CFTR, TCR subunits, hERG/ERG-type K+ channels) in the ER via preferential interaction with their transmembrane segments; beyond classical ER quality control, calnexin undergoes KAT7-mediated K525 crotonylation that drives its lysosomal translocation to inhibit Ragulator-RRAG GTPase activity and suppress leucine-stimulated mTORC1, interacts with ULK1 at the ER to support autophagy initiation, and forms a complex with FAM134B and LC3 at ER–endolysosome membrane contact sites to mediate ERLAD of misfolded polymers; its stability is regulated by CBL- and TRIM27-mediated ubiquitination, and its transcriptional output includes suppression of IRF7 via HDAC3 recruitment.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"Calnexin (CANX/IP90/p88) is an ER transmembrane chaperone that mediates quality control of newly synthesized membrane proteins by retaining and stabilizing incompletely assembled or misfolded intermediates in the ER until proper assembly is achieved [#0, #2]. It associates transiently with a broad range of ER-transiting proteins and holds onto unassembled subunits—peptide-deficient MHC class I heavy chain–β2-microglobulin heterodimers and free heavy chains, unassembled TCR β-chains, and partially assembled MHC class II α/β/invariant-chain complexes—releasing them only upon completion of assembly and ER egress [#0, #2, #3]. This recognition is directed primarily at the transmembrane segment and flanking residues of client proteins rather than their luminal domains, as GPI-anchored class I variants fail to bind calnexin unless engineered to carry a transmembrane region [#4]. Through this activity calnexin supports biogenesis and surface delivery of clients including ΔF508-sensitive CFTR [#1], ERG/hERG-type K+ channels where it facilitates tetrameric assembly [#5], and cell-surface MHC-I, with calnexin levels setting MHC-I display and consequent CD8+ T-cell-mediated cytotoxicity [#7, #13]. Beyond classical ER quality control, calnexin acts in protein-degradation and autophagy pathways: it partners with the ER-phagy receptor FAM134B and LC3 at ER–endolysosome membrane contact sites to drive ERLAD of misfolded alpha-1-antitrypsin (ATZ) polymers [#9], serves as an interaction partner required for ULK1 recruitment to the ER and for autophagy initiation [#8], and—following KAT7-mediated K525 crotonylation—translocates to lysosomes where it binds LAMP2 and inhibits Ragulator GEF activity toward RRAG GTPases to suppress leucine-stimulated mTORC1 [#6]. Calnexin abundance is controlled by ubiquitin-mediated degradation via the E3 ligases CBL and TRIM27 [#10, #11], and it can repress IRF7 transcription by recruiting HDAC3 to the IRF7 promoter [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Established calnexin as a general ER retention chaperone by showing it transiently binds many nascent ER-transiting proteins and stably holds unassembled subunits when assembly partners are absent.\",\n      \"evidence\": \"Pulse-chase metabolic labeling and co-immunoprecipitation of unassembled TCR β-chains with IP90 in T cell lines\",\n      \"pmids\": [\"8486646\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define the structural basis of client recognition\", \"Single-lab co-IP without reconstitution\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Resolved how calnexin recognizes clients, showing the interaction is mediated by the transmembrane segment and flanking residues rather than the luminal domain.\",\n      \"evidence\": \"Domain-deletion mutagenesis, GPI-anchor substitution hybrids, and co-IP with class I heavy chains and TCR α-chain\",\n      \"pmids\": [\"8349678\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address calnexin's lectin/glycan-dependent recognition mode\", \"Mapped on a limited set of clients\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Demonstrated a functional consequence of calnexin binding—retention and protection of MHC class I assembly intermediates and partially assembled class II complexes, slowing transport and impeding degradation until assembly completes.\",\n      \"evidence\": \"Heterologous reconstitution in Drosophila cells with transport assays, and pulse-chase co-IP tracking class II assembly intermediates\",\n      \"pmids\": [\"8278813\", \"8313912\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of release upon completed assembly not defined\", \"Quantitative contribution to degradation kinetics not isolated\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Extended calnexin's quality-control role to a disease-relevant client, showing it discriminates wild-type from misfolded CFTR by retaining the misfolded form in the ER.\",\n      \"evidence\": \"Co-immunoprecipitation and glycerol density gradient cosedimentation of nascent CFTR in epithelial and CHO cells\",\n      \"pmids\": [\"7513695\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish whether retention promotes folding or commits CFTR to degradation\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showed calnexin actively assists multimeric channel assembly, not merely retention, by facilitating tetramerization of ERG-type K+ channels and being required for hERG surface expression.\",\n      \"evidence\": \"C. elegans forward genetic screen, liposome-assisted cell-free assembly assay, calnexin KO with electrophysiology, and co-IP across species\",\n      \"pmids\": [\"29941431\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of assembly assistance not resolved\", \"Whether assembly chaperoning generalizes to other tetrameric channels unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified upstream regulation of calnexin by miR-148a-3p, linking calnexin abundance to MHC-I surface levels and antitumor immunity.\",\n      \"evidence\": \"Luciferase reporter validation of miRNA targeting, CANX knockdown/rescue, and CD8+ T cell cytotoxicity assays with in vivo tumor models\",\n      \"pmids\": [\"34324740\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not establish the molecular step at which calnexin controls MHC-I trafficking\", \"Single-lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed a non-canonical calnexin function as a negative regulator of nutrient signaling, showing crotonylation-driven lysosomal translocation inhibits Ragulator GEF activity to suppress leucine-stimulated mTORC1.\",\n      \"evidence\": \"Cell-free mTORC1 reconstitution, lysosomal fractionation, CANX–LAMP2 and CANX–Ragulator co-IPs, mass spectrometry of K525 crotonylation, and KAT7 KO with functional rescue\",\n      \"pmids\": [\"35266843\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How an ER membrane protein relocates to lysosomes mechanistically unresolved\", \"Crosstalk with calnexin's ER chaperone pool unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Provided gain- and loss-of-function evidence that calnexin sets MHC-I surface levels and tunes CD8+ T-cell killing in colorectal cancer.\",\n      \"evidence\": \"Lentiviral overexpression and siRNA knockdown with MHC-I Western blot, CD8+ T cell co-culture cytotoxicity, and cytokine ELISA\",\n      \"pmids\": [\"35356876\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic step controlling surface MHC-I not pinpointed\", \"Single-lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed calnexin upstream of autophagy initiation by identifying it as a ULK1 partner required for ULK1 recruitment to the ER, with in vivo cognitive consequences in an AD model.\",\n      \"evidence\": \"Co-IP, proximity ligation, BiFC, CANX KO in hippocampal neurons with LC3/flux assays, domain-deletion rescue, and Morris water maze testing\",\n      \"pmids\": [\"39813987\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural ULK1-binding determinant within calnexin not mapped\", \"Relationship to calnexin's chaperone function unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected calnexin to ER-to-lysosome degradation by showing it forms a segregation complex with FAM134B and LC3 at ER–endolysosome contact sites to deliver misfolded ATZ polymers for degradation.\",\n      \"evidence\": \"Fluorescence microscopy of membrane contact sites, proximity assays, and ATZ fate tracking with manipulation of CANX, FAM134B, VAPA, ORP1L, RAB7\",\n      \"pmids\": [\"41179805\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding interfaces within the complex not defined\", \"Single study\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Characterized post-translational control of calnexin stability, identifying CBL and TRIM27 as E3 ligases that ubiquitinate and degrade calnexin, and a transcriptional repressor role via HDAC3 recruitment to IRF7.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, chromatin-associated HDAC3 assays at the IRF7 promoter, and CANX knockdown/overexpression in tumor cells with PI3K/AKT readouts\",\n      \"pmids\": [\"40514420\", \"41557161\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitination sites not mapped\", \"TRIM27 link rests on co-IP/ubiquitination without mutagenesis or reconstitution\", \"How an ER chaperone reaches gene promoters mechanistically unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How calnexin partitions between its canonical ER chaperone pool and its non-canonical roles at lysosomes, ER-phagy contact sites, and gene promoters—and how post-translational marks like K525 crotonylation switch between these functions—remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model linking client recognition to relocalization\", \"Quantitative flux of calnexin between compartments unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [0, 2, 3, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1, 2, 8]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [6, 9]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 7, 13]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [8, 9]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6, 11]}\n    ],\n    \"complexes\": [\n      \"CANX–FAM134B–LC3 ER-phagy segregation complex\"\n    ],\n    \"partners\": [\n      \"LAMP2\",\n      \"RRAGA\",\n      \"ULK1\",\n      \"FAM134B\",\n      \"MAP1LC3B\",\n      \"CBL\",\n      \"HDAC3\",\n      \"TRIM27\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}