{"gene":"ENTR1","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2016,"finding":"SDCCAG3 localizes to the basal body of primary cilia and is required for normal ciliary length and the percentage of ciliated cells. SDCCAG3 interacts with the intraflagellar transport protein IFT88 via its N-terminus, which binds to a region of IFT88 containing tetratricopeptide (TRP) repeats. SDCCAG3 knockdown reduces ciliary localization of the membrane protein Polycystin-2 but does not affect ciliary Rab8.","method":"Immunofluorescence localization, siRNA knockdown with ciliary length/percentage quantification, co-immunoprecipitation (Co-IP), domain mapping pulldown experiments","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and domain mapping plus functional knockdown phenotype in single lab with multiple orthogonal methods","pmids":["27767179"],"is_preprint":false},{"year":2024,"finding":"DLG1 functions upstream of SDCCAG3 in a pathway controlling ciliary protein trafficking: loss of DLG1 reduces SDCCAG3, IFT20, and polycystin-2 in cilia. Biochemical and AlphaFold modelling approaches indicate that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Re-expression of wild-type DLG1, but not the CAKUT-associated p.T489R variant, rescues the ciliary phenotype.","method":"Conditional Dlg1 knockout mouse, proximity-labeling proteomics (BioID), fluorescence microscopy, biochemical Co-IP, AlphaFold structural modelling, rescue experiments with DLG1 wild-type vs. variant","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional KO replicated with multiple orthogonal methods (proteomics, microscopy, biochemistry, genetic rescue), confirmed in peer-reviewed publication and preprint","pmids":["38849673","37987012"],"is_preprint":false},{"year":2024,"finding":"ENTR1 binds PPARγ and enhances its expression, thereby elevating downstream adipogenic markers C/EBPα and LDLR. ENTR1 gain- and loss-of-function both enhance lipid droplet formation in bone marrow mesenchymal stem cells (BMSCs). The small molecule AN698/40746067 targets ENTR1 to suppress PPARγ and attenuates adipogenesis in vitro and bone marrow adiposity/bone loss in vivo.","method":"Co-immunoprecipitation (ENTR1-PPARγ interaction), gain- and loss-of-function assays in BMSCs, lipid droplet staining, Western blot for downstream markers, in vivo hyperlipidemia mouse model","journal":"Biomedicine & pharmacotherapy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus bidirectional functional assays in single lab with in vivo validation","pmids":["38810405"],"is_preprint":false},{"year":2025,"finding":"SDCCAG3 enhances PPARγ stability in adipocytes by preventing its ubiquitin-proteasome-mediated degradation through SMURF1 (an E3 ubiquitin ligase). PPARγ in turn negatively transcriptionally regulates SDCCAG3, forming a SDCCAG3-PPARγ-SDCCAG3 feedback loop. Adipose-specific SDCCAG3 knockout in mice fed a high-fat diet results in pathological adipose expansion and metabolic dysfunction.","method":"Adipose-specific conditional knockout mice (high-fat diet model), adipose-specific overexpression mouse model, Western blot for PPARγ ubiquitination/degradation, co-immunoprecipitation (SDCCAG3-SMURF1-PPARγ), transcriptional regulation assays","journal":"Journal of lipid research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo conditional KO and OE with mechanistic Co-IP, single lab, multiple orthogonal methods","pmids":["40058593"],"is_preprint":false},{"year":2025,"finding":"ENTR1 directly interacts with AMPK and enhances its phosphorylation (activation). Overexpression of ENTR1 suppresses macrophage M1 polarization and mitigates bone loss in a ligature-induced periodontitis mouse model, while knockdown exacerbates these effects. The inhibitory effect of ENTR1 on M1 polarization and bone resorption is partially attenuated by the AMPK inhibitor Compound C, confirming AMPK as mediator.","method":"Co-immunoprecipitation (ENTR1-AMPK), Western blot for AMPK phosphorylation, ENTR1 overexpression/knockdown in macrophages under inflammatory stimuli, pharmacological inhibition with Compound C, ligature-induced periodontitis mouse model, micro-CT and histological staining","journal":"Life sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional rescue with pharmacological inhibitor and in vivo model, single lab","pmids":["40054733"],"is_preprint":false},{"year":2025,"finding":"ENTR1 stabilizes MAVS on mitochondria by suppressing NIX-mediated mitophagy. ENTR1 knockout increases NIX accumulation on mitochondria, promoting autophagic degradation of MAVS and impairing type I interferon (IFN-I) signaling, thereby allowing greater BPIV3 and VSV replication. Silencing NIX in ENTR1-deficient cells rescues MAVS protein levels and reduces viral titers.","method":"ENTR1 knockout cells, viral infection assay (BPIV3, VSV), Western blot for MAVS/NIX, mitophagy flux assays, siRNA knockdown of NIX as epistasis rescue experiment, immunofluorescence","journal":"Veterinary microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis (NIX knockdown rescue) combined with loss-of-function KO and viral replication readout, single lab","pmids":["41494271"],"is_preprint":false},{"year":2025,"finding":"ENTR1 knockout in HCT-116 colon cancer cells reduces proliferation and downregulates key glycolytic enzyme expression levels, indicating that ENTR1 promotes colon cancer cell growth by regulating glycolysis.","method":"CRISPR/gene knockout of ENTR1 in HCT-116 cells, cell proliferation assays, Western blot for glycolytic enzymes","journal":"BMC cancer","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single knockout cell line experiment, no mechanistic pathway placement beyond enzyme expression change","pmids":["40462015"],"is_preprint":false}],"current_model":"ENTR1/SDCCAG3 is an endosomal/trafficking regulator that localizes to the basal body of primary cilia (where it interacts with IFT88 and, together with IFT20, acts downstream of DLG1 to traffic polycystin-2 to cilia), interacts with AMPK to suppress macrophage M1 polarization, binds PPARγ and SMURF1 to modulate adipogenesis, stabilizes the antiviral signaling protein MAVS by suppressing NIX-dependent mitophagy to promote IFN-I responses, and supports colon cancer cell proliferation by regulating glycolytic enzyme expression."},"narrative":{"mechanistic_narrative":"ENTR1 (SDCCAG3) is a multifunctional trafficking and protein-stability regulator that operates at the primary cilium, in metabolic and immune signaling, and in cancer cell metabolism [PMID:27767179, PMID:40058593]. At the ciliary basal body it interacts with the intraflagellar transport protein IFT88 through its N-terminus and is required for normal ciliary length, ciliation, and the ciliary delivery of the membrane protein polycystin-2 [PMID:27767179]; it acts within a DLG1-dependent pathway, forming a complex with IFT20 that associates with DLG1 to control ciliary trafficking of polycystin-2, a pathway disrupted by a CAKUT-associated DLG1 variant [PMID:38849673, PMID:37987012]. In metabolism, ENTR1 binds PPARγ and enhances its abundance, stabilizing PPARγ by antagonizing SMURF1-mediated ubiquitin-proteasome degradation within a reciprocal feedback loop that drives adipogenesis, with adipose-specific loss causing pathological adipose expansion and metabolic dysfunction [PMID:38810405, PMID:40058593]. ENTR1 also acts as a positive regulator of innate signaling: it interacts with AMPK and enhances its activating phosphorylation to suppress macrophage M1 polarization [PMID:40054733], and it stabilizes mitochondrial MAVS by suppressing NIX-mediated mitophagy to sustain type I interferon responses and restrict viral replication [PMID:41494271]. A recurring theme across these roles is control of partner protein stability and intracellular localization.","teleology":[{"year":2016,"claim":"Established ENTR1/SDCCAG3 as a basal-body component required for ciliogenesis and selective ciliary cargo delivery, answering whether the protein has a defined role at the cilium.","evidence":"Immunofluorescence localization, siRNA knockdown with ciliary quantification, and reciprocal Co-IP/domain mapping with IFT88 in cultured cells","pmids":["27767179"],"confidence":"Medium","gaps":["Mechanism by which the SDCCAG3-IFT88 interaction promotes polycystin-2 trafficking not resolved","Single-lab Co-IP without orthogonal interaction validation","No structural detail of the N-terminus/TPR-repeat contact"]},{"year":2024,"claim":"Placed SDCCAG3 within an upstream-to-downstream trafficking hierarchy, showing DLG1 governs SDCCAG3/IFT20/polycystin-2 ciliary delivery and linking the pathway to disease via a CAKUT variant.","evidence":"Conditional Dlg1 knockout mouse, BioID proximity proteomics, Co-IP, AlphaFold modelling, and genetic rescue with DLG1 wild-type vs variant","pmids":["38849673","37987012"],"confidence":"High","gaps":["SDCCAG3-DLG1 association shown only as indirect/at least partially indirect","Direct molecular bridge between the SDCCAG3-IFT20 complex and DLG1 not defined"]},{"year":2024,"claim":"Identified a metabolic role by showing ENTR1 binds PPARγ and enhances its expression to drive adipogenic differentiation, and demonstrated druggability.","evidence":"Co-IP, bidirectional gain/loss-of-function in BMSCs with lipid droplet staining, and a small-molecule ENTR1 ligand tested in a hyperlipidemia mouse model","pmids":["38810405"],"confidence":"Medium","gaps":["Mechanism by which both gain and loss of function enhance lipid droplet formation not reconciled","Direct vs indirect nature of PPARγ regulation not resolved at this stage"]},{"year":2025,"claim":"Defined the molecular basis of ENTR1-PPARγ regulation as stabilization against SMURF1-dependent degradation within a reciprocal feedback loop, advancing from correlation to mechanism.","evidence":"Adipose-specific conditional knockout and overexpression mice on high-fat diet, PPARγ ubiquitination/degradation Western blots, SDCCAG3-SMURF1-PPARγ Co-IP, and transcriptional assays","pmids":["40058593"],"confidence":"Medium","gaps":["Whether ENTR1 acts as a direct SMURF1 competitor or scaffold not established","Single-lab mechanism"]},{"year":2025,"claim":"Extended ENTR1 to inflammatory signaling by showing it interacts with AMPK and enhances its activating phosphorylation to suppress macrophage M1 polarization and bone loss.","evidence":"Co-IP, AMPK phosphorylation Westerns, overexpression/knockdown in macrophages, Compound C epistasis, and a ligature-induced periodontitis mouse model","pmids":["40054733"],"confidence":"Medium","gaps":["How ENTR1 binding enhances AMPK phosphorylation mechanistically unknown","Direct vs indirect kinase activation not distinguished"]},{"year":2025,"claim":"Established an antiviral role by showing ENTR1 stabilizes mitochondrial MAVS through suppression of NIX-mediated mitophagy to sustain type I interferon responses.","evidence":"ENTR1 knockout cells, BPIV3/VSV infection assays, mitophagy flux readouts, and NIX-knockdown epistasis rescue of MAVS levels and viral titers","pmids":["41494271"],"confidence":"Medium","gaps":["How ENTR1 restrains NIX accumulation on mitochondria not defined","Single-lab loss-of-function model"]},{"year":2025,"claim":"Linked ENTR1 to cancer cell metabolism, showing its loss reduces colon cancer proliferation and glycolytic enzyme expression.","evidence":"CRISPR knockout in HCT-116 cells with proliferation assays and glycolytic enzyme Westerns","pmids":["40462015"],"confidence":"Low","gaps":["No mechanistic pathway placement beyond enzyme expression change","Single cell line, single lab","Whether the glycolytic effect is direct or downstream of another ENTR1 function unknown"]},{"year":null,"claim":"Whether ENTR1's diverse roles (ciliary trafficking, PPARγ/AMPK regulation, MAVS stabilization, glycolysis) reflect a single unifying biochemical activity remains unresolved.","evidence":"No discovery in the corpus tests a common molecular mechanism across these contexts","pmids":[],"confidence":"Low","gaps":["No defined enzymatic or core biochemical activity shared across functions","No structural model of the protein","Tissue-specific determinants of which pathway ENTR1 engages are unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140313","term_label":"molecular sequestering activity","supporting_discovery_ids":[3,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,3,4]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[4,5]}],"complexes":[],"partners":["IFT88","DLG1","IFT20","PPARG","SMURF1","AMPK","MAVS"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96C92","full_name":"Endosome-associated-trafficking regulator 1","aliases":["Antigen NY-CO-3","Serologically defined colon cancer antigen 3"],"length_aa":435,"mass_kda":48.0,"function":"Endosome-associated protein that plays a role in membrane receptor sorting, cytokinesis and ciliogenesis (PubMed:23108400, PubMed:25278552, PubMed:27767179). Involved in the endosome-to-plasma membrane trafficking and recycling of SNX27-retromer-dependent cargo proteins, such as GLUT1 (PubMed:25278552). Involved in the regulation of cytokinesis; the function may involve PTPN13 and GIT1 (PubMed:23108400). Plays a role in the formation of cilia (PubMed:27767179). Involved in cargo protein localization, such as PKD2, at primary cilia (PubMed:27767179). Involved in the presentation of the tumor necrosis factor (TNF) receptor TNFRSF1A on the cell surface, and hence in the modulation of the TNF-induced apoptosis (By similarity)","subcellular_location":"Cytoplasm; Early endosome; Endosome; Recycling endosome; Midbody; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Cytoplasm, cytoskeleton, cilium basal body","url":"https://www.uniprot.org/uniprotkb/Q96C92/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ENTR1","classification":"Not Classified","n_dependent_lines":7,"n_total_lines":1208,"dependency_fraction":0.005794701986754967},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2},{"gene":"MIF","stoichiometry":0.2},{"gene":"RBM14","stoichiometry":0.2},{"gene":"VPS35","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ENTR1","total_profiled":1310},"omim":[{"mim_id":"618289","title":"ENDOSOME-ASSOCIATED TRAFFICKING REGULATOR 1; ENTR1","url":"https://www.omim.org/entry/618289"}],"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/ENTR1"},"hgnc":{"alias_symbol":["NY-CO-3"],"prev_symbol":["SDCCAG3"]},"alphafold":{"accession":"Q96C92","domains":[{"cath_id":"1.20.5","chopping":"262-381","consensus_level":"medium","plddt":96.8596,"start":262,"end":381}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96C92","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96C92-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96C92-F1-predicted_aligned_error_v6.png","plddt_mean":64.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ENTR1","jax_strain_url":"https://www.jax.org/strain/search?query=ENTR1"},"sequence":{"accession":"Q96C92","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96C92.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96C92/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96C92"}},"corpus_meta":[{"pmid":"27767179","id":"PMC_27767179","title":"The serologically defined colon cancer antigen-3 (SDCCAG3) is involved in the regulation of ciliogenesis.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27767179","citation_count":15,"is_preprint":false},{"pmid":"32339468","id":"PMC_32339468","title":"Sdccag3 Promotes Implant Osseointegration during Experimental Hyperlipidemia.","date":"2020","source":"Journal of dental research","url":"https://pubmed.ncbi.nlm.nih.gov/32339468","citation_count":13,"is_preprint":false},{"pmid":"38849673","id":"PMC_38849673","title":"DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2.","date":"2024","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/38849673","citation_count":8,"is_preprint":false},{"pmid":"35812058","id":"PMC_35812058","title":"Long non-coding RNA lncHUPC1 induced by FOXA1 promotes tumor progression by inhibiting apoptosis via miR-133b/SDCCAG3 in prostate cancer.","date":"2022","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/35812058","citation_count":6,"is_preprint":false},{"pmid":"38810405","id":"PMC_38810405","title":"AN698/40746067 suppresses bone marrow adiposity to ameliorate hyperlipidemia-induced osteoporosis through targeted inhibition of ENTR1.","date":"2024","source":"Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/38810405","citation_count":5,"is_preprint":false},{"pmid":"40058593","id":"PMC_40058593","title":"SDCCAG3 inhibits adipocyte hypertrophy and improves obesity-related metabolic disorders via SDCCAG3/SMURF1/PPARγ axis.","date":"2025","source":"Journal of lipid research","url":"https://pubmed.ncbi.nlm.nih.gov/40058593","citation_count":1,"is_preprint":false},{"pmid":"40462015","id":"PMC_40462015","title":"ENTR1 affects the progression of colon cancer by regulating energy metabolism under the influence of glycolysis.","date":"2025","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40462015","citation_count":1,"is_preprint":false},{"pmid":"40054733","id":"PMC_40054733","title":"ENTR1 regulates periodontitis by modulating macrophage M1 polarization via AMPK activation.","date":"2025","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40054733","citation_count":1,"is_preprint":false},{"pmid":"41494271","id":"PMC_41494271","title":"ENTR1 stabilizes MAVS by inhibiting NIX-mediated mitophagy to restrict BPIV3 and VSV replication.","date":"2025","source":"Veterinary microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/41494271","citation_count":1,"is_preprint":false},{"pmid":"37987012","id":"PMC_37987012","title":"DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37987012","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7570,"output_tokens":2140,"usd":0.027405,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9209,"output_tokens":2960,"usd":0.060022,"stage2_stop_reason":"end_turn"},"total_usd":0.087427,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"SDCCAG3 localizes to the basal body of primary cilia and is required for normal ciliary length and the percentage of ciliated cells. SDCCAG3 interacts with the intraflagellar transport protein IFT88 via its N-terminus, which binds to a region of IFT88 containing tetratricopeptide (TRP) repeats. SDCCAG3 knockdown reduces ciliary localization of the membrane protein Polycystin-2 but does not affect ciliary Rab8.\",\n      \"method\": \"Immunofluorescence localization, siRNA knockdown with ciliary length/percentage quantification, co-immunoprecipitation (Co-IP), domain mapping pulldown experiments\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and domain mapping plus functional knockdown phenotype in single lab with multiple orthogonal methods\",\n      \"pmids\": [\"27767179\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DLG1 functions upstream of SDCCAG3 in a pathway controlling ciliary protein trafficking: loss of DLG1 reduces SDCCAG3, IFT20, and polycystin-2 in cilia. Biochemical and AlphaFold modelling approaches indicate that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Re-expression of wild-type DLG1, but not the CAKUT-associated p.T489R variant, rescues the ciliary phenotype.\",\n      \"method\": \"Conditional Dlg1 knockout mouse, proximity-labeling proteomics (BioID), fluorescence microscopy, biochemical Co-IP, AlphaFold structural modelling, rescue experiments with DLG1 wild-type vs. variant\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional KO replicated with multiple orthogonal methods (proteomics, microscopy, biochemistry, genetic rescue), confirmed in peer-reviewed publication and preprint\",\n      \"pmids\": [\"38849673\", \"37987012\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ENTR1 binds PPARγ and enhances its expression, thereby elevating downstream adipogenic markers C/EBPα and LDLR. ENTR1 gain- and loss-of-function both enhance lipid droplet formation in bone marrow mesenchymal stem cells (BMSCs). The small molecule AN698/40746067 targets ENTR1 to suppress PPARγ and attenuates adipogenesis in vitro and bone marrow adiposity/bone loss in vivo.\",\n      \"method\": \"Co-immunoprecipitation (ENTR1-PPARγ interaction), gain- and loss-of-function assays in BMSCs, lipid droplet staining, Western blot for downstream markers, in vivo hyperlipidemia mouse model\",\n      \"journal\": \"Biomedicine & pharmacotherapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus bidirectional functional assays in single lab with in vivo validation\",\n      \"pmids\": [\"38810405\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SDCCAG3 enhances PPARγ stability in adipocytes by preventing its ubiquitin-proteasome-mediated degradation through SMURF1 (an E3 ubiquitin ligase). PPARγ in turn negatively transcriptionally regulates SDCCAG3, forming a SDCCAG3-PPARγ-SDCCAG3 feedback loop. Adipose-specific SDCCAG3 knockout in mice fed a high-fat diet results in pathological adipose expansion and metabolic dysfunction.\",\n      \"method\": \"Adipose-specific conditional knockout mice (high-fat diet model), adipose-specific overexpression mouse model, Western blot for PPARγ ubiquitination/degradation, co-immunoprecipitation (SDCCAG3-SMURF1-PPARγ), transcriptional regulation assays\",\n      \"journal\": \"Journal of lipid research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo conditional KO and OE with mechanistic Co-IP, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"40058593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ENTR1 directly interacts with AMPK and enhances its phosphorylation (activation). Overexpression of ENTR1 suppresses macrophage M1 polarization and mitigates bone loss in a ligature-induced periodontitis mouse model, while knockdown exacerbates these effects. The inhibitory effect of ENTR1 on M1 polarization and bone resorption is partially attenuated by the AMPK inhibitor Compound C, confirming AMPK as mediator.\",\n      \"method\": \"Co-immunoprecipitation (ENTR1-AMPK), Western blot for AMPK phosphorylation, ENTR1 overexpression/knockdown in macrophages under inflammatory stimuli, pharmacological inhibition with Compound C, ligature-induced periodontitis mouse model, micro-CT and histological staining\",\n      \"journal\": \"Life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional rescue with pharmacological inhibitor and in vivo model, single lab\",\n      \"pmids\": [\"40054733\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ENTR1 stabilizes MAVS on mitochondria by suppressing NIX-mediated mitophagy. ENTR1 knockout increases NIX accumulation on mitochondria, promoting autophagic degradation of MAVS and impairing type I interferon (IFN-I) signaling, thereby allowing greater BPIV3 and VSV replication. Silencing NIX in ENTR1-deficient cells rescues MAVS protein levels and reduces viral titers.\",\n      \"method\": \"ENTR1 knockout cells, viral infection assay (BPIV3, VSV), Western blot for MAVS/NIX, mitophagy flux assays, siRNA knockdown of NIX as epistasis rescue experiment, immunofluorescence\",\n      \"journal\": \"Veterinary microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis (NIX knockdown rescue) combined with loss-of-function KO and viral replication readout, single lab\",\n      \"pmids\": [\"41494271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ENTR1 knockout in HCT-116 colon cancer cells reduces proliferation and downregulates key glycolytic enzyme expression levels, indicating that ENTR1 promotes colon cancer cell growth by regulating glycolysis.\",\n      \"method\": \"CRISPR/gene knockout of ENTR1 in HCT-116 cells, cell proliferation assays, Western blot for glycolytic enzymes\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single knockout cell line experiment, no mechanistic pathway placement beyond enzyme expression change\",\n      \"pmids\": [\"40462015\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ENTR1/SDCCAG3 is an endosomal/trafficking regulator that localizes to the basal body of primary cilia (where it interacts with IFT88 and, together with IFT20, acts downstream of DLG1 to traffic polycystin-2 to cilia), interacts with AMPK to suppress macrophage M1 polarization, binds PPARγ and SMURF1 to modulate adipogenesis, stabilizes the antiviral signaling protein MAVS by suppressing NIX-dependent mitophagy to promote IFN-I responses, and supports colon cancer cell proliferation by regulating glycolytic enzyme expression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ENTR1 (SDCCAG3) is a multifunctional trafficking and protein-stability regulator that operates at the primary cilium, in metabolic and immune signaling, and in cancer cell metabolism [#0, #3]. At the ciliary basal body it interacts with the intraflagellar transport protein IFT88 through its N-terminus and is required for normal ciliary length, ciliation, and the ciliary delivery of the membrane protein polycystin-2 [#0]; it acts within a DLG1-dependent pathway, forming a complex with IFT20 that associates with DLG1 to control ciliary trafficking of polycystin-2, a pathway disrupted by a CAKUT-associated DLG1 variant [#1]. In metabolism, ENTR1 binds PPARγ and enhances its abundance, stabilizing PPARγ by antagonizing SMURF1-mediated ubiquitin-proteasome degradation within a reciprocal feedback loop that drives adipogenesis, with adipose-specific loss causing pathological adipose expansion and metabolic dysfunction [#2, #3]. ENTR1 also acts as a positive regulator of innate signaling: it interacts with AMPK and enhances its activating phosphorylation to suppress macrophage M1 polarization [#4], and it stabilizes mitochondrial MAVS by suppressing NIX-mediated mitophagy to sustain type I interferon responses and restrict viral replication [#5]. A recurring theme across these roles is control of partner protein stability and intracellular localization.\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established ENTR1/SDCCAG3 as a basal-body component required for ciliogenesis and selective ciliary cargo delivery, answering whether the protein has a defined role at the cilium.\",\n      \"evidence\": \"Immunofluorescence localization, siRNA knockdown with ciliary quantification, and reciprocal Co-IP/domain mapping with IFT88 in cultured cells\",\n      \"pmids\": [\"27767179\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which the SDCCAG3-IFT88 interaction promotes polycystin-2 trafficking not resolved\", \"Single-lab Co-IP without orthogonal interaction validation\", \"No structural detail of the N-terminus/TPR-repeat contact\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed SDCCAG3 within an upstream-to-downstream trafficking hierarchy, showing DLG1 governs SDCCAG3/IFT20/polycystin-2 ciliary delivery and linking the pathway to disease via a CAKUT variant.\",\n      \"evidence\": \"Conditional Dlg1 knockout mouse, BioID proximity proteomics, Co-IP, AlphaFold modelling, and genetic rescue with DLG1 wild-type vs variant\",\n      \"pmids\": [\"38849673\", \"37987012\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"SDCCAG3-DLG1 association shown only as indirect/at least partially indirect\", \"Direct molecular bridge between the SDCCAG3-IFT20 complex and DLG1 not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified a metabolic role by showing ENTR1 binds PPARγ and enhances its expression to drive adipogenic differentiation, and demonstrated druggability.\",\n      \"evidence\": \"Co-IP, bidirectional gain/loss-of-function in BMSCs with lipid droplet staining, and a small-molecule ENTR1 ligand tested in a hyperlipidemia mouse model\",\n      \"pmids\": [\"38810405\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which both gain and loss of function enhance lipid droplet formation not reconciled\", \"Direct vs indirect nature of PPARγ regulation not resolved at this stage\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the molecular basis of ENTR1-PPARγ regulation as stabilization against SMURF1-dependent degradation within a reciprocal feedback loop, advancing from correlation to mechanism.\",\n      \"evidence\": \"Adipose-specific conditional knockout and overexpression mice on high-fat diet, PPARγ ubiquitination/degradation Western blots, SDCCAG3-SMURF1-PPARγ Co-IP, and transcriptional assays\",\n      \"pmids\": [\"40058593\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ENTR1 acts as a direct SMURF1 competitor or scaffold not established\", \"Single-lab mechanism\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended ENTR1 to inflammatory signaling by showing it interacts with AMPK and enhances its activating phosphorylation to suppress macrophage M1 polarization and bone loss.\",\n      \"evidence\": \"Co-IP, AMPK phosphorylation Westerns, overexpression/knockdown in macrophages, Compound C epistasis, and a ligature-induced periodontitis mouse model\",\n      \"pmids\": [\"40054733\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How ENTR1 binding enhances AMPK phosphorylation mechanistically unknown\", \"Direct vs indirect kinase activation not distinguished\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established an antiviral role by showing ENTR1 stabilizes mitochondrial MAVS through suppression of NIX-mediated mitophagy to sustain type I interferon responses.\",\n      \"evidence\": \"ENTR1 knockout cells, BPIV3/VSV infection assays, mitophagy flux readouts, and NIX-knockdown epistasis rescue of MAVS levels and viral titers\",\n      \"pmids\": [\"41494271\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How ENTR1 restrains NIX accumulation on mitochondria not defined\", \"Single-lab loss-of-function model\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linked ENTR1 to cancer cell metabolism, showing its loss reduces colon cancer proliferation and glycolytic enzyme expression.\",\n      \"evidence\": \"CRISPR knockout in HCT-116 cells with proliferation assays and glycolytic enzyme Westerns\",\n      \"pmids\": [\"40462015\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanistic pathway placement beyond enzyme expression change\", \"Single cell line, single lab\", \"Whether the glycolytic effect is direct or downstream of another ENTR1 function unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether ENTR1's diverse roles (ciliary trafficking, PPARγ/AMPK regulation, MAVS stabilization, glycolysis) reflect a single unifying biochemical activity remains unresolved.\",\n      \"evidence\": \"No discovery in the corpus tests a common molecular mechanism across these contexts\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No defined enzymatic or core biochemical activity shared across functions\", \"No structural model of the protein\", \"Tissue-specific determinants of which pathway ENTR1 engages are unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140313\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 3, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"IFT88\", \"DLG1\", \"IFT20\", \"PPARG\", \"SMURF1\", \"AMPK\", \"MAVS\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}