{"gene":"HEATR3","run_date":"2026-06-10T01:55:22","timeline":{"discoveries":[{"year":2022,"finding":"HEATR3 is required for the nucleolar surveillance pathway that stabilizes p53; genome-wide loss-of-function screens identified HEATR3 as critical for regulating this pathway, and selectively disabling it abolishes the ability of nuclear-acting stresses (including DNA damage) to induce p53 accumulation.","method":"Genome-wide loss-of-function (CRISPR) screens; selective genetic disruption of nucleolar surveillance pathway with p53 stabilization readout","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide functional screen with mechanistic follow-up in single study; p53 readout validated but mechanistic detail limited to abstract","pmids":["36323262"],"is_preprint":false},{"year":2022,"finding":"HEATR3 functions as a nuclear import chaperone for ribosomal proteins uL18 (RPL5) and uL5 (RPL11); loss-of-function variants in HEATR3 reduce nuclear accumulation of uL18, impair pre-rRNA processing and ribosomal subunit formation, and cause Diamond-Blackfan anemia with abnormal erythrocyte maturation and proliferation defects independent of p53 activation.","method":"Patient-derived fibroblasts and hematopoietic progenitor cells with HEATR3 variants; shRNA knockdown; immunofluorescence for nuclear uL18 localization; yeast model complementation; rRNA processing assays; flow cytometry for erythroid differentiation","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (patient cells, shRNA KD, yeast models, nuclear localization assay, rRNA processing), replicated across cell types and organisms","pmids":["35213692"],"is_preprint":false},{"year":2013,"finding":"HEATR3 plays a positive role in NOD2-mediated NF-κB signaling, as demonstrated by expression studies; a missense variant R642S in HEATR3 was associated with Crohn's disease in Ashkenazi Jewish individuals.","method":"Expression/reporter studies of HEATR3 in NOD2-mediated NF-κB signaling; haplotype association and exome sequencing","journal":"Genes and immunity","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited mechanistic detail in abstract ('expression studies' without specification of assay type or controls)","pmids":["23615072"],"is_preprint":false},{"year":2023,"finding":"HEATR3 knockdown in bladder cancer cells inhibits proliferation, invasion, and migration, blocks cell cycle progression, promotes apoptosis, and reduces phosphorylation of AKT and ERK, placing HEATR3 upstream of AKT/ERK signaling in these cells.","method":"siRNA knockdown in BCa cell lines (5637, TCCSUP, SW780); CCK8 proliferation assay; Transwell migration/invasion; flow cytometry for cell cycle and apoptosis; Western blot for p-AKT and p-ERK","journal":"Molecular genetics and genomics : MGG","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, multiple cellular readouts but no direct biochemical mechanism linking HEATR3 to AKT/ERK; pathway placement inferred indirectly","pmids":["37518364"],"is_preprint":false},{"year":2025,"finding":"HEATR3 acts as a receptor for selective autophagy (xenophagy): it contains an LC3-interacting region (LIR), localizes to intracellularly invading Salmonella and chemically damaged lysosomes, recruits LC3 to damaged membranes, and facilitates delivery of targets to lysosomes. HEATR3 deficiency promotes Salmonella proliferation in the cytoplasm and impairs LC3 recruitment. Rescue with wild-type but not LIR-mutant HEATR3 confirms the LIR-LC3 interaction is essential. HEATR3 recruitment to damaged membranes is upstream of ATG5/FIP200 but dependent on calcium signaling.","method":"Quantitative mass spectrometry identification; HEATR3 KO cells; fluorescence microscopy for HEATR3 and LC3 localization; Salmonella proliferation assay; chemical lysosome damage model; rescue with wild-type vs. LIR-mutant HEATR3; ATG5/FIP200 KO epistasis; calcium chelator treatment","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (KO, rescue, mutagenesis of LIR, epistasis with ATG5/FIP200, calcium chelation), clear mechanistic hierarchy established in single rigorous study","pmids":["40178893"],"is_preprint":false},{"year":2025,"finding":"HEATR3 serves as a host nuclear transport adaptor for the Legionella effector Ceg10, mediating its nuclear import; HEATR3 physically interacts with Ceg10 to facilitate its entry into the nucleus where it acetylates RPS20.","method":"Structural analysis of Ceg10; nuclear import assay; identification of HEATR3 as transport adaptor via co-immunoprecipitation/pulldown (implied by mechanistic characterization in the study)","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — structural and functional study establishing HEATR3 as nuclear import adaptor for a bacterial effector, single study with multiple methods but mechanistic detail about HEATR3 itself is secondary to the main Ceg10 characterization","pmids":["41468429"],"is_preprint":false},{"year":2025,"finding":"LMAN2 physically interacts with HEATR3 (confirmed by co-immunoprecipitation), and HEATR3 overexpression reverses the suppressive effects of LMAN2 knockdown on HER2-positive breast cancer cell proliferation, migration, invasion, AKT/ERK/NF-κB signaling, and inflammatory cytokine production.","method":"Co-immunoprecipitation; Western blot; siRNA knockdown of LMAN2 with HEATR3 overexpression rescue; CCK-8, EdU, wound healing, Transwell assays; ELISA for cytokines","journal":"Biochemistry and cell biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Co-IP establishes interaction but the mechanistic role of HEATR3 in this context is inferred from rescue experiments without direct biochemical characterization of the interaction's functional consequence","pmids":["39772898"],"is_preprint":false}],"current_model":"HEATR3 is a multifunctional HEAT-repeat protein that acts as a nuclear import chaperone for ribosomal proteins uL18 (RPL5) and uL5 (RPL11) to support ribosome biogenesis and nucleolar surveillance-dependent p53 stabilization; serves as a selective autophagy receptor via its LIR motif to recruit LC3 to damaged membranes and invading bacteria (xenophagy); functions as a nuclear transport adaptor for at least one bacterial effector protein; and positively modulates NOD2-mediated NF-κB signaling, with loss-of-function variants causing Diamond-Blackfan anemia."},"narrative":{"mechanistic_narrative":"HEATR3 is a multifunctional HEAT-repeat protein that links ribosome biogenesis surveillance to selective autophagy and innate immune signaling. In ribosome biogenesis, HEATR3 acts as a nuclear import chaperone for the ribosomal proteins uL18 (RPL5) and uL5 (RPL11); loss-of-function variants reduce nuclear accumulation of uL18, impair pre-rRNA processing and ribosomal subunit formation, and cause Diamond-Blackfan anemia with defective erythroid maturation independent of p53 activation [PMID:35213692]. Consistent with this role at the nucleolar surveillance interface, HEATR3 is required for the nucleolar surveillance pathway that stabilizes p53, such that its disruption abolishes p53 accumulation in response to nuclear-acting stresses including DNA damage [PMID:36323262]. Independently, HEATR3 functions as a selective autophagy (xenophagy) receptor: it carries an LC3-interacting region (LIR), localizes to invading Salmonella and chemically damaged lysosomes, and recruits LC3 to damaged membranes to drive their lysosomal delivery, acting upstream of ATG5/FIP200 in a calcium-dependent manner [PMID:40178893]. HEATR3 also serves as a host nuclear transport adaptor that physically binds the Legionella effector Ceg10 to mediate its nuclear import [PMID:41468429]. The mechanistic basis by which HEATR3 modulates downstream signaling outputs has not been characterized in the available corpus.","teleology":[{"year":2013,"claim":"First functional link, addressing whether HEATR3 participates in innate immune signaling, placed it as a positive modulator of NOD2-mediated NF-κB activation and tied a missense variant to Crohn's disease.","evidence":"Expression/reporter studies of NOD2 signaling plus haplotype association and exome sequencing in Ashkenazi Jewish individuals","pmids":["23615072"],"confidence":"Low","gaps":["Single lab with unspecified reporter assay details and controls","No direct biochemical interaction between HEATR3 and NOD2 demonstrated","Disease association not mechanistically connected to the signaling readout"]},{"year":2022,"claim":"Two 2022 studies established HEATR3's core cellular role: it is a nuclear import chaperone for uL18/uL5 required for ribosome biogenesis, and it is required for the nucleolar surveillance pathway that stabilizes p53.","evidence":"Patient-derived cells with HEATR3 variants, shRNA knockdown, yeast complementation, nuclear uL18 immunofluorescence and rRNA processing assays; separately, genome-wide CRISPR loss-of-function screens with a p53 stabilization readout","pmids":["35213692","36323262"],"confidence":"High","gaps":["Structural basis of uL18/uL5 recognition not resolved","Mechanistic detail of how HEATR3 loss blocks p53 stabilization limited","Relationship between the chaperone function and the p53 surveillance role not directly tested in one system"]},{"year":2023,"claim":"A cancer-cell study asked whether HEATR3 influences proliferative signaling, finding its knockdown suppresses growth, invasion, and migration and reduces AKT/ERK phosphorylation in bladder cancer cells.","evidence":"siRNA knockdown in bladder cancer lines with proliferation, migration/invasion, cell cycle, apoptosis assays and Western blot for p-AKT/p-ERK","pmids":["37518364"],"confidence":"Low","gaps":["No direct biochemical link between HEATR3 and AKT/ERK demonstrated","Pathway placement inferred indirectly from phenotypes","Single lab without orthogonal validation"]},{"year":2025,"claim":"HEATR3 was defined as a selective autophagy receptor, answering how damaged membranes and cytosolic bacteria are targeted to lysosomes: it uses a LIR motif to recruit LC3 upstream of ATG5/FIP200.","evidence":"Quantitative mass spectrometry, HEATR3 KO and rescue with wild-type vs LIR-mutant, fluorescence microscopy, Salmonella proliferation assay, lysosome damage model, ATG5/FIP200 epistasis and calcium chelation","pmids":["40178893"],"confidence":"High","gaps":["Upstream sensor coupling HEATR3 to calcium signaling not identified","Structural basis of LIR-LC3 interaction not resolved","Relationship to HEATR3's ribosomal/nuclear roles unexplored"]},{"year":2025,"claim":"HEATR3 was shown to act as a host nuclear transport adaptor co-opted by a bacterial effector, addressing how Legionella Ceg10 reaches the nucleus to acetylate RPS20.","evidence":"Structural analysis of Ceg10, nuclear import assays, and HEATR3 interaction identification by co-immunoprecipitation/pulldown","pmids":["41468429"],"confidence":"Medium","gaps":["HEATR3 characterization is secondary to the Ceg10 study","Whether HEATR3 functions as a general nuclear import adaptor for host cargo beyond ribosomal proteins not established","Interface mapping of the HEATR3-Ceg10 interaction not detailed"]},{"year":null,"claim":"It remains unresolved how HEATR3's distinct roles — ribosomal protein import, nucleolar p53 surveillance, LIR-dependent autophagy, and bacterial effector transport — are mechanistically integrated by a single HEAT-repeat scaffold.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model unifying its cargo-binding and LIR functions","Whether the autophagy and ribosome roles share a common surface or are mutually exclusive is unknown","Direct mechanism connecting HEATR3 to NF-κB and AKT/ERK signaling outputs not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140104","term_label":"molecular carrier activity","supporting_discovery_ids":[1,5]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,5]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4]}],"complexes":[],"partners":["RPL5","RPL11","LC3","CEG10","LMAN2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q7Z4Q2","full_name":"HEAT repeat-containing protein 3","aliases":["Symportin Syo1","hsSyo1"],"length_aa":680,"mass_kda":74.6,"function":"Plays a role in ribosome biogenesis and in nuclear import of the 60S ribosomal protein L5/large ribosomal subunit protein uL18 (RPL5) (PubMed:35213692). Required for proper erythrocyte maturation (PubMed:35213692)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q7Z4Q2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/HEATR3","classification":"Not Classified","n_dependent_lines":347,"n_total_lines":1208,"dependency_fraction":0.28725165562913907},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000155393","cell_line_id":"CID000967","localizations":[{"compartment":"nucleoplasm","grade":3},{"compartment":"cytoplasmic","grade":2}],"interactors":[{"gene":"RPL11","stoichiometry":10.0},{"gene":"CLIP1","stoichiometry":0.2},{"gene":"DHX9","stoichiometry":0.2},{"gene":"ESD","stoichiometry":0.2},{"gene":"ACADM","stoichiometry":0.2},{"gene":"PNPT1","stoichiometry":0.2},{"gene":"NDUFAF2","stoichiometry":0.2},{"gene":"C1QBP","stoichiometry":0.2},{"gene":"TRAP1","stoichiometry":0.2},{"gene":"HNRNPA0","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000967","total_profiled":1310},"omim":[{"mim_id":"620072","title":"DIAMOND-BLACKFAN ANEMIA 21; DBA21","url":"https://www.omim.org/entry/620072"},{"mim_id":"614951","title":"HEAT REPEAT-CONTAINING PROTEIN 3; HEATR3","url":"https://www.omim.org/entry/614951"},{"mim_id":"105650","title":"DIAMOND-BLACKFAN ANEMIA 1; DBA1","url":"https://www.omim.org/entry/105650"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/HEATR3"},"hgnc":{"alias_symbol":["FLJ20718"],"prev_symbol":[]},"alphafold":{"accession":"Q7Z4Q2","domains":[{"cath_id":"1.25.10.10","chopping":"42-142_150-185","consensus_level":"medium","plddt":92.1318,"start":42,"end":185},{"cath_id":"1.25.10,1.25.40","chopping":"537-680","consensus_level":"medium","plddt":92.7378,"start":537,"end":680}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z4Q2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z4Q2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z4Q2-F1-predicted_aligned_error_v6.png","plddt_mean":83.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HEATR3","jax_strain_url":"https://www.jax.org/strain/search?query=HEATR3"},"sequence":{"accession":"Q7Z4Q2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q7Z4Q2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q7Z4Q2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z4Q2"}},"corpus_meta":[{"pmid":"36323262","id":"PMC_36323262","title":"Nuclear stabilization of p53 requires a functional nucleolar surveillance pathway.","date":"2022","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36323262","citation_count":43,"is_preprint":false},{"pmid":"31249589","id":"PMC_31249589","title":"A Trans-Ethnic Genome-Wide Association Study of Uterine Fibroids.","date":"2019","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31249589","citation_count":39,"is_preprint":false},{"pmid":"35213692","id":"PMC_35213692","title":"HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia.","date":"2022","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/35213692","citation_count":33,"is_preprint":false},{"pmid":"23615072","id":"PMC_23615072","title":"Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3.","date":"2013","source":"Genes and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/23615072","citation_count":27,"is_preprint":false},{"pmid":"26770579","id":"PMC_26770579","title":"Genetic variants at 6p21, 10q23, 16q21 and 22q12 are associated with esophageal cancer risk in a Chinese Han population.","date":"2015","source":"International journal of clinical and experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26770579","citation_count":14,"is_preprint":false},{"pmid":"33936159","id":"PMC_33936159","title":"Meta-Analyses of Splicing and Expression Quantitative Trait Loci Identified Susceptibility Genes of Glioma.","date":"2021","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33936159","citation_count":11,"is_preprint":false},{"pmid":"40050615","id":"PMC_40050615","title":"Genome-wide meta-analysis identifies novel risk loci for uterine fibroids within and across multiple ancestry groups.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/40050615","citation_count":7,"is_preprint":false},{"pmid":"38002903","id":"PMC_38002903","title":"The Diverse Genomic Landscape of Diamond-Blackfan Anemia: Two Novel Variants and a Mini-Review.","date":"2023","source":"Children (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/38002903","citation_count":6,"is_preprint":false},{"pmid":"37085538","id":"PMC_37085538","title":"Role of DNA methylation in the relationship between glioma risk factors and glioma incidence: a two-step Mendelian randomization study.","date":"2023","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/37085538","citation_count":5,"is_preprint":false},{"pmid":"37518364","id":"PMC_37518364","title":"HEATR3 involved in the cell proliferation, metastasis and cell cycle development of bladder cancer acts as a tumor suppressor.","date":"2023","source":"Molecular genetics and genomics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/37518364","citation_count":4,"is_preprint":false},{"pmid":"36338958","id":"PMC_36338958","title":"Candidate genes and sequence variants for susceptibility to mycobacterial infection identified by whole-exome sequencing.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36338958","citation_count":4,"is_preprint":false},{"pmid":"40178893","id":"PMC_40178893","title":"HEATR3 recognizes membrane rupture and facilitates xenophagy in response to Salmonella invasion.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/40178893","citation_count":3,"is_preprint":false},{"pmid":"39772898","id":"PMC_39772898","title":"LMAN2 interacts with HEATR3 to expedite HER2-positive breast cancer advancement and inflammation and Akt/ERK/NF-κB signaling.","date":"2025","source":"Biochemistry and cell biology = Biochimie et biologie cellulaire","url":"https://pubmed.ncbi.nlm.nih.gov/39772898","citation_count":1,"is_preprint":false},{"pmid":"41468429","id":"PMC_41468429","title":"Legionella effector Ceg10 acetylates RPS20 to inhibit host translation and induce cell cycle arrest.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/41468429","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9984,"output_tokens":2089,"usd":0.030644,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9090,"output_tokens":2611,"usd":0.055363,"stage2_stop_reason":"end_turn"},"total_usd":0.086007,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"HEATR3 is required for the nucleolar surveillance pathway that stabilizes p53; genome-wide loss-of-function screens identified HEATR3 as critical for regulating this pathway, and selectively disabling it abolishes the ability of nuclear-acting stresses (including DNA damage) to induce p53 accumulation.\",\n      \"method\": \"Genome-wide loss-of-function (CRISPR) screens; selective genetic disruption of nucleolar surveillance pathway with p53 stabilization readout\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide functional screen with mechanistic follow-up in single study; p53 readout validated but mechanistic detail limited to abstract\",\n      \"pmids\": [\"36323262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"HEATR3 functions as a nuclear import chaperone for ribosomal proteins uL18 (RPL5) and uL5 (RPL11); loss-of-function variants in HEATR3 reduce nuclear accumulation of uL18, impair pre-rRNA processing and ribosomal subunit formation, and cause Diamond-Blackfan anemia with abnormal erythrocyte maturation and proliferation defects independent of p53 activation.\",\n      \"method\": \"Patient-derived fibroblasts and hematopoietic progenitor cells with HEATR3 variants; shRNA knockdown; immunofluorescence for nuclear uL18 localization; yeast model complementation; rRNA processing assays; flow cytometry for erythroid differentiation\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (patient cells, shRNA KD, yeast models, nuclear localization assay, rRNA processing), replicated across cell types and organisms\",\n      \"pmids\": [\"35213692\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"HEATR3 plays a positive role in NOD2-mediated NF-κB signaling, as demonstrated by expression studies; a missense variant R642S in HEATR3 was associated with Crohn's disease in Ashkenazi Jewish individuals.\",\n      \"method\": \"Expression/reporter studies of HEATR3 in NOD2-mediated NF-κB signaling; haplotype association and exome sequencing\",\n      \"journal\": \"Genes and immunity\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited mechanistic detail in abstract ('expression studies' without specification of assay type or controls)\",\n      \"pmids\": [\"23615072\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"HEATR3 knockdown in bladder cancer cells inhibits proliferation, invasion, and migration, blocks cell cycle progression, promotes apoptosis, and reduces phosphorylation of AKT and ERK, placing HEATR3 upstream of AKT/ERK signaling in these cells.\",\n      \"method\": \"siRNA knockdown in BCa cell lines (5637, TCCSUP, SW780); CCK8 proliferation assay; Transwell migration/invasion; flow cytometry for cell cycle and apoptosis; Western blot for p-AKT and p-ERK\",\n      \"journal\": \"Molecular genetics and genomics : MGG\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, multiple cellular readouts but no direct biochemical mechanism linking HEATR3 to AKT/ERK; pathway placement inferred indirectly\",\n      \"pmids\": [\"37518364\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HEATR3 acts as a receptor for selective autophagy (xenophagy): it contains an LC3-interacting region (LIR), localizes to intracellularly invading Salmonella and chemically damaged lysosomes, recruits LC3 to damaged membranes, and facilitates delivery of targets to lysosomes. HEATR3 deficiency promotes Salmonella proliferation in the cytoplasm and impairs LC3 recruitment. Rescue with wild-type but not LIR-mutant HEATR3 confirms the LIR-LC3 interaction is essential. HEATR3 recruitment to damaged membranes is upstream of ATG5/FIP200 but dependent on calcium signaling.\",\n      \"method\": \"Quantitative mass spectrometry identification; HEATR3 KO cells; fluorescence microscopy for HEATR3 and LC3 localization; Salmonella proliferation assay; chemical lysosome damage model; rescue with wild-type vs. LIR-mutant HEATR3; ATG5/FIP200 KO epistasis; calcium chelator treatment\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (KO, rescue, mutagenesis of LIR, epistasis with ATG5/FIP200, calcium chelation), clear mechanistic hierarchy established in single rigorous study\",\n      \"pmids\": [\"40178893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HEATR3 serves as a host nuclear transport adaptor for the Legionella effector Ceg10, mediating its nuclear import; HEATR3 physically interacts with Ceg10 to facilitate its entry into the nucleus where it acetylates RPS20.\",\n      \"method\": \"Structural analysis of Ceg10; nuclear import assay; identification of HEATR3 as transport adaptor via co-immunoprecipitation/pulldown (implied by mechanistic characterization in the study)\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — structural and functional study establishing HEATR3 as nuclear import adaptor for a bacterial effector, single study with multiple methods but mechanistic detail about HEATR3 itself is secondary to the main Ceg10 characterization\",\n      \"pmids\": [\"41468429\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LMAN2 physically interacts with HEATR3 (confirmed by co-immunoprecipitation), and HEATR3 overexpression reverses the suppressive effects of LMAN2 knockdown on HER2-positive breast cancer cell proliferation, migration, invasion, AKT/ERK/NF-κB signaling, and inflammatory cytokine production.\",\n      \"method\": \"Co-immunoprecipitation; Western blot; siRNA knockdown of LMAN2 with HEATR3 overexpression rescue; CCK-8, EdU, wound healing, Transwell assays; ELISA for cytokines\",\n      \"journal\": \"Biochemistry and cell biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Co-IP establishes interaction but the mechanistic role of HEATR3 in this context is inferred from rescue experiments without direct biochemical characterization of the interaction's functional consequence\",\n      \"pmids\": [\"39772898\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"HEATR3 is a multifunctional HEAT-repeat protein that acts as a nuclear import chaperone for ribosomal proteins uL18 (RPL5) and uL5 (RPL11) to support ribosome biogenesis and nucleolar surveillance-dependent p53 stabilization; serves as a selective autophagy receptor via its LIR motif to recruit LC3 to damaged membranes and invading bacteria (xenophagy); functions as a nuclear transport adaptor for at least one bacterial effector protein; and positively modulates NOD2-mediated NF-κB signaling, with loss-of-function variants causing Diamond-Blackfan anemia.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"HEATR3 is a multifunctional HEAT-repeat protein that links ribosome biogenesis surveillance to selective autophagy and innate immune signaling. In ribosome biogenesis, HEATR3 acts as a nuclear import chaperone for the ribosomal proteins uL18 (RPL5) and uL5 (RPL11); loss-of-function variants reduce nuclear accumulation of uL18, impair pre-rRNA processing and ribosomal subunit formation, and cause Diamond-Blackfan anemia with defective erythroid maturation independent of p53 activation [#1]. Consistent with this role at the nucleolar surveillance interface, HEATR3 is required for the nucleolar surveillance pathway that stabilizes p53, such that its disruption abolishes p53 accumulation in response to nuclear-acting stresses including DNA damage [#0]. Independently, HEATR3 functions as a selective autophagy (xenophagy) receptor: it carries an LC3-interacting region (LIR), localizes to invading Salmonella and chemically damaged lysosomes, and recruits LC3 to damaged membranes to drive their lysosomal delivery, acting upstream of ATG5/FIP200 in a calcium-dependent manner [#4]. HEATR3 also serves as a host nuclear transport adaptor that physically binds the Legionella effector Ceg10 to mediate its nuclear import [#5]. The mechanistic basis by which HEATR3 modulates downstream signaling outputs has not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"First functional link, addressing whether HEATR3 participates in innate immune signaling, placed it as a positive modulator of NOD2-mediated NF-\\u03baB activation and tied a missense variant to Crohn's disease.\",\n      \"evidence\": \"Expression/reporter studies of NOD2 signaling plus haplotype association and exome sequencing in Ashkenazi Jewish individuals\",\n      \"pmids\": [\"23615072\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single lab with unspecified reporter assay details and controls\", \"No direct biochemical interaction between HEATR3 and NOD2 demonstrated\", \"Disease association not mechanistically connected to the signaling readout\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Two 2022 studies established HEATR3's core cellular role: it is a nuclear import chaperone for uL18/uL5 required for ribosome biogenesis, and it is required for the nucleolar surveillance pathway that stabilizes p53.\",\n      \"evidence\": \"Patient-derived cells with HEATR3 variants, shRNA knockdown, yeast complementation, nuclear uL18 immunofluorescence and rRNA processing assays; separately, genome-wide CRISPR loss-of-function screens with a p53 stabilization readout\",\n      \"pmids\": [\"35213692\", \"36323262\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of uL18/uL5 recognition not resolved\", \"Mechanistic detail of how HEATR3 loss blocks p53 stabilization limited\", \"Relationship between the chaperone function and the p53 surveillance role not directly tested in one system\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"A cancer-cell study asked whether HEATR3 influences proliferative signaling, finding its knockdown suppresses growth, invasion, and migration and reduces AKT/ERK phosphorylation in bladder cancer cells.\",\n      \"evidence\": \"siRNA knockdown in bladder cancer lines with proliferation, migration/invasion, cell cycle, apoptosis assays and Western blot for p-AKT/p-ERK\",\n      \"pmids\": [\"37518364\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct biochemical link between HEATR3 and AKT/ERK demonstrated\", \"Pathway placement inferred indirectly from phenotypes\", \"Single lab without orthogonal validation\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"HEATR3 was defined as a selective autophagy receptor, answering how damaged membranes and cytosolic bacteria are targeted to lysosomes: it uses a LIR motif to recruit LC3 upstream of ATG5/FIP200.\",\n      \"evidence\": \"Quantitative mass spectrometry, HEATR3 KO and rescue with wild-type vs LIR-mutant, fluorescence microscopy, Salmonella proliferation assay, lysosome damage model, ATG5/FIP200 epistasis and calcium chelation\",\n      \"pmids\": [\"40178893\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Upstream sensor coupling HEATR3 to calcium signaling not identified\", \"Structural basis of LIR-LC3 interaction not resolved\", \"Relationship to HEATR3's ribosomal/nuclear roles unexplored\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"HEATR3 was shown to act as a host nuclear transport adaptor co-opted by a bacterial effector, addressing how Legionella Ceg10 reaches the nucleus to acetylate RPS20.\",\n      \"evidence\": \"Structural analysis of Ceg10, nuclear import assays, and HEATR3 interaction identification by co-immunoprecipitation/pulldown\",\n      \"pmids\": [\"41468429\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"HEATR3 characterization is secondary to the Ceg10 study\", \"Whether HEATR3 functions as a general nuclear import adaptor for host cargo beyond ribosomal proteins not established\", \"Interface mapping of the HEATR3-Ceg10 interaction not detailed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how HEATR3's distinct roles \\u2014 ribosomal protein import, nucleolar p53 surveillance, LIR-dependent autophagy, and bacterial effector transport \\u2014 are mechanistically integrated by a single HEAT-repeat scaffold.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model unifying its cargo-binding and LIR functions\", \"Whether the autophagy and ribosome roles share a common surface or are mutually exclusive is unknown\", \"Direct mechanism connecting HEATR3 to NF-\\u03baB and AKT/ERK signaling outputs not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140104\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RPL5\", \"RPL11\", \"LC3\", \"Ceg10\", \"LMAN2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}