{"gene":"LARP4B","run_date":"2026-06-10T02:59:49","timeline":{"discoveries":[{"year":2015,"finding":"LARP4B binds to 3' UTRs of a distinct set of cellular mRNAs, with a defined AU-rich binding motif identified by PAR-CLIP and in vitro binding assays; reduction of LARP4B destabilizes these mRNA targets and reduces their translation.","method":"PAR-CLIP transcriptome-wide analysis, biocomputational motif analysis, in vitro binding assays, knockdown with mRNA stability and proteome readout","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — PAR-CLIP (transcriptome-wide), in vitro binding assays, and functional knockdown with two orthogonal readouts (mRNA stability and translation), multiple methods in one study","pmids":["26001795"],"is_preprint":false},{"year":2016,"finding":"The La module (LA motif + adjacent RRM) of LARP4B is required for its growth-suppressive activity and directly associates with BAX mRNA, as shown by mutagenesis and RNA association assays in glioma cells.","method":"La module deletion mutagenesis, RNA immunoprecipitation/association assay, overexpression in glioma cell lines with proliferation/apoptosis readout","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mutagenesis plus mRNA association, single lab with two orthogonal methods","pmids":["26933087"],"is_preprint":false},{"year":2020,"finding":"The crystal structure of the variant PAM2w motif in the N-terminal region of LARP4B bound to the MLLE domain of PABPC1 revealed a new mode of PAM2–MLLE interaction; mutational studies in vitro and in vivo confirmed the structural contacts are required for binding.","method":"X-ray crystallography, mutational analysis in vitro and in vivo","journal":"Biomolecules","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with mutational validation both in vitro and in vivo, orthogonal methods in one rigorous study","pmids":["32517187"],"is_preprint":false},{"year":2018,"finding":"In Drosophila, overexpression of Larp4B reduces cell and organ size; this effect requires the LA motif and RRM RNA-binding domains and is mediated by downregulation of dMyc protein levels. Loss-of-function mutation of larp4B increases dMyc protein. Genetic epistasis showed that dMyc overexpression suppresses the larp4B-overexpression phenotype.","method":"Transgenic overexpression, deletion mutant transgenes, genetic epistasis (dMyc suppressor), Western blot for dMyc protein","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis plus domain mutagenesis and protein level readout, single lab","pmids":["29462618"],"is_preprint":false},{"year":2024,"finding":"LARP4B binds to SPINK1 mRNA via its La motif and stabilizes it, thereby activating the SPINK1–EGFR signaling pathway to promote HCC progression. LARP4B expression is upregulated in HCC via METTL3-mediated m6A modification recognized by IGF2BP3.","method":"RNA immunoprecipitation sequencing, RIP-seq, RNA pulldown, gain- and loss-of-function assays, in vivo xenograft, EGFR pathway readout","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP-seq plus functional assays, single lab with multiple orthogonal methods","pmids":["38693111"],"is_preprint":false},{"year":2024,"finding":"LARP4B binds to WNK1 mRNA and promotes its stability; stabilized WNK1 competitively binds the Kelch domain of Keap1, promoting NRF2 nuclear translocation and activation of the NRF2/GCH1/BH4 pathway, thereby inhibiting ferroptosis in pancreatic cancer cells.","method":"RNA binding/RIP assay for WNK1 mRNA, NRF2 nuclear translocation assay, NRF2 inhibitor (ML385) rescue, ROS/MDA/GSH/SOD measurements, in vivo xenograft","journal":"Integrative biology : quantitative biosciences from nano to macro","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP plus pharmacological rescue and multiple orthogonal functional readouts, single lab","pmids":["41014504"],"is_preprint":false},{"year":2024,"finding":"LARP4B (and LARP4) conserved region-2 (CR2), specifically positions 615–625, directly binds RACK1 region 200–317 (a ribosome-associated protein); CR2 mutations decrease LARP4B association with RACK1 and ribosomes, impair stabilization of AU-rich element (ARE)-containing mRNAs, and reduce translation efficiency of ARE-containing reporters. AlphaFold2-multimer predicted high-confidence interaction of CR2 with RACK1 propellers 5–6, consistent with experimental results.","method":"Yeast two-hybrid domain mapping, co-immunoprecipitation, polysome profiling, β-globin-ARE mRNA reporter assay, nanoLuc-ARE luciferase assay, CR2 mutagenesis, AlphaFold2-multimer structural prediction","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid plus Co-IP, ribosome association, and reporter translation assays with mutagenesis; preprint, single lab, multiple orthogonal methods","pmids":["bio_10.1101_2024.11.01.621267"],"is_preprint":true},{"year":2024,"finding":"LARP4B (but not LARP4A) specifically regulates cell cycle progression in osteosarcoma and prostate cancer cells, modulating key cell cycle proteins including Cyclins B1 and E2, Aurora B, and E2F1, as determined by transcriptomic profiling and high-content multiparametric analyses following LARP4B depletion.","method":"siRNA/shRNA depletion, transcriptomic profiling, high-content multiparametric imaging analysis, xenograft models","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with defined cellular phenotype and transcriptomic profiling, single lab, two orthogonal readouts","pmids":["38532886"],"is_preprint":false},{"year":2013,"finding":"Knockdown of Larp4b in mouse Lin(-) hematopoietic progenitor cells did not affect colony-forming ability, apoptosis, or cell cycle in vitro (negative result).","method":"Lentiviral shRNA knockdown in mouse Lin(-) cells, colony forming cell assay, AnnexinV/PI staining, RT-PCR","journal":"Zhongguo shi yan xue ye xue za zhi","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single method (colony assay), single lab, negative result only","pmids":["23815932"],"is_preprint":false}],"current_model":"LARP4B is an RNA-binding protein that uses its La module (LA motif + RRM) to bind AU-rich sequences in the 3' UTRs of target mRNAs, stabilizing them and promoting their translation; it physically interacts with PABPC1 via a variant PAM2w motif (crystal structure resolved) and with ribosome-associated RACK1 via a conserved region-2 (CR2), the latter interaction promoting translational efficiency especially of ARE-containing mRNAs; LARP4B also stabilizes specific oncogenic mRNAs (e.g., SPINK1, WNK1) to activate downstream signaling pathways, and its RNA-binding domains are required for its roles in regulating cell growth, cell cycle, and dMyc levels."},"narrative":{"mechanistic_narrative":"LARP4B is an RNA-binding protein that selects a defined set of cellular mRNAs through their 3' UTRs and acts post-transcriptionally to stabilize them and promote their translation [PMID:26001795]. Target recognition is mediated by its La module (the LA motif plus adjacent RRM), which binds an AU-rich sequence motif and is required both for direct mRNA association and for LARP4B's effects on cell growth [PMID:26001795, PMID:26933087]. LARP4B is integrated into the translational machinery through two protein contacts: its N-terminal variant PAM2w motif engages the MLLE domain of the poly(A)-binding protein PABPC1 in a structurally distinct PAM2–MLLE mode [PMID:32517187], and its conserved region-2 directly binds the ribosome-associated protein RACK1, an interaction that enhances stabilization and translation efficiency of ARE-containing mRNAs [PMID:bio_10.1101_2024.11.01.621267]. Through these activities LARP4B controls cell and organ size and cell cycle progression: in Drosophila its growth-suppressive effect depends on the LA motif and RRM and operates by lowering dMyc protein levels [PMID:29462618], while in human tumor cells its depletion deregulates cell-cycle regulators including Cyclins B1 and E2, Aurora B, and E2F1 [PMID:38532886]. In cancer contexts LARP4B stabilizes specific oncogenic transcripts—SPINK1 to drive SPINK1–EGFR signaling in hepatocellular carcinoma and WNK1 to engage the Keap1/NRF2/GCH1/BH4 axis and suppress ferroptosis in pancreatic cancer—linking its mRNA-stabilizing function to downstream signaling outputs [PMID:38693111, PMID:41014504].","teleology":[{"year":2013,"claim":"An early loss-of-function test asked whether LARP4B is required for hematopoietic progenitor function, establishing a context-dependent rather than universal cellular requirement.","evidence":"Lentiviral shRNA knockdown in mouse Lin(-) progenitor cells with colony-forming, apoptosis, and cell-cycle readouts","pmids":["23815932"],"confidence":"Low","gaps":["Negative result from a single colony-forming assay; does not exclude roles in other cell types or molecular functions","No molecular target or binding activity tested","No protein-level or stability readout"]},{"year":2015,"claim":"Defined LARP4B's core molecular activity by identifying its transcriptome-wide mRNA targets and showing it stabilizes them and promotes their translation, establishing it as a 3' UTR-binding post-transcriptional regulator.","evidence":"PAR-CLIP transcriptome-wide mapping, motif analysis, in vitro binding, and knockdown with mRNA-stability and proteome readouts","pmids":["26001795"],"confidence":"High","gaps":["Did not resolve which protein partners couple binding to stabilization/translation","AU-rich motif defined but structural basis of recognition not determined"]},{"year":2016,"claim":"Localized the RNA-binding and growth-regulatory function to the La module, linking a specific domain to direct mRNA association and a cellular phenotype.","evidence":"La module deletion mutagenesis and RNA association assays with proliferation/apoptosis readout in glioma cells","pmids":["26933087"],"confidence":"Medium","gaps":["Single target mRNA (BAX) tested for association","Single lab; mechanism connecting La-module binding to growth suppression not fully resolved"]},{"year":2018,"claim":"Provided in vivo genetic evidence that LARP4B controls organismal growth, defining dMyc as a key downstream effector and confirming the RNA-binding domains are required.","evidence":"Drosophila transgenic overexpression and loss-of-function, domain-deletion transgenes, dMyc genetic epistasis, and Western blot","pmids":["29462618"],"confidence":"Medium","gaps":["Whether dMyc regulation is direct (mRNA binding) versus indirect not resolved","Mammalian conservation of the dMyc/MYC axis not tested here"]},{"year":2020,"claim":"Resolved the structural basis of the LARP4B–PABPC1 interaction, revealing a variant PAM2w–MLLE binding mode and validating the contacts functionally.","evidence":"X-ray crystallography of the PAM2w–MLLE complex with mutational analysis in vitro and in vivo","pmids":["32517187"],"confidence":"High","gaps":["Functional consequence of disrupting PABPC1 binding on specific mRNA targets not detailed","How this contact integrates with La-module mRNA binding not addressed"]},{"year":2024,"claim":"Identified RACK1 as a direct ribosome-associated partner via conserved region-2, mechanistically coupling LARP4B to the ribosome and to ARE-mRNA stabilization and translation.","evidence":"Yeast two-hybrid domain mapping, Co-IP, polysome profiling, ARE reporter assays, CR2 mutagenesis, and AlphaFold2-multimer prediction (preprint)","pmids":["bio_10.1101_2024.11.01.621267"],"confidence":"Medium","gaps":["Preprint, single lab; structural prediction not experimentally validated","Reciprocal endogenous interaction and stoichiometry on ribosomes not established"]},{"year":2024,"claim":"Established LARP4B as a paralog-specific cell-cycle regulator, distinguishing its function from LARP4A and identifying affected cell-cycle proteins.","evidence":"siRNA/shRNA depletion with transcriptomic profiling, high-content multiparametric imaging, and xenografts in osteosarcoma and prostate cancer cells","pmids":["38532886"],"confidence":"Medium","gaps":["Whether cell-cycle gene changes are direct mRNA targets versus secondary not resolved","Single lab"]},{"year":2024,"claim":"Connected LARP4B's mRNA-stabilizing activity to defined oncogenic signaling outputs by showing it stabilizes specific transcripts to drive disease-relevant pathways.","evidence":"RIP-seq/RIP, RNA pulldown, gain/loss-of-function, pathway readouts (SPINK1–EGFR; WNK1–Keap1/NRF2/GCH1/BH4 ferroptosis), and xenografts in HCC and pancreatic cancer","pmids":["38693111","41014504"],"confidence":"Medium","gaps":["Each axis shown in a single tumor context by a single lab","Generality of these targets across tissues not established"]},{"year":null,"claim":"How the La-module mRNA recognition, PABPC1 binding, and RACK1/ribosome coupling are integrated into a unified mechanism that selects which target mRNAs are stabilized versus translationally enhanced in a given cell type remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No integrated structural/biochemical model linking all three binding activities on a single mRNP","Rules governing target selectivity across tissues not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,4,5,6]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[0,6]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,6]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[3,7]}],"complexes":[],"partners":["PABPC1","RACK1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q92615","full_name":"La-related protein 4B","aliases":["La ribonucleoprotein domain family member 4B","La ribonucleoprotein domain family member 5","La-related protein 5"],"length_aa":738,"mass_kda":80.6,"function":"Stimulates mRNA translation","subcellular_location":"Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/Q92615/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LARP4B","classification":"Not Classified","n_dependent_lines":15,"n_total_lines":1208,"dependency_fraction":0.012417218543046357},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2},{"gene":"G3BP2","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"RBM42","stoichiometry":0.2},{"gene":"RBM8A","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2},{"gene":"SRP9","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/LARP4B","total_profiled":1310},"omim":[{"mim_id":"616513","title":"La RIBONUCLEOPROTEIN 4B; LARP4B","url":"https://www.omim.org/entry/616513"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Cytosol","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/LARP4B"},"hgnc":{"alias_symbol":[],"prev_symbol":["KIAA0217","LARP5"]},"alphafold":{"accession":"Q92615","domains":[{"cath_id":"1.10.10.10","chopping":"156-233","consensus_level":"medium","plddt":90.1814,"start":156,"end":233},{"cath_id":"3.30.70.330","chopping":"234-317","consensus_level":"medium","plddt":86.1605,"start":234,"end":317}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q92615","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q92615-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q92615-F1-predicted_aligned_error_v6.png","plddt_mean":52.78},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LARP4B","jax_strain_url":"https://www.jax.org/strain/search?query=LARP4B"},"sequence":{"accession":"Q92615","fasta_url":"https://rest.uniprot.org/uniprotkb/Q92615.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q92615/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q92615"}},"corpus_meta":[{"pmid":"26933087","id":"PMC_26933087","title":"Identification of RNA-Binding Protein LARP4B as a Tumor Suppressor in Glioma.","date":"2016","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/26933087","citation_count":43,"is_preprint":false},{"pmid":"26001795","id":"PMC_26001795","title":"LARP4B is an AU-rich sequence associated factor that promotes mRNA accumulation and translation.","date":"2015","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/26001795","citation_count":43,"is_preprint":false},{"pmid":"31173237","id":"PMC_31173237","title":"MicroRNA‑106b functions as an oncogene and regulates tumor viability and metastasis by targeting LARP4B in prostate cancer.","date":"2019","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/31173237","citation_count":16,"is_preprint":false},{"pmid":"38693111","id":"PMC_38693111","title":"LARP4B promotes hepatocellular carcinoma progression and impairs sorafenib efficacy by activating SPINK1-mediated EGFR pathway.","date":"2024","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/38693111","citation_count":15,"is_preprint":false},{"pmid":"38532886","id":"PMC_38532886","title":"The RNA binding proteins LARP4A and LARP4B promote sarcoma and carcinoma growth and metastasis.","date":"2024","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/38532886","citation_count":13,"is_preprint":false},{"pmid":"32517187","id":"PMC_32517187","title":"Crystal Structure of a Variant PAM2 Motif of LARP4B Bound to the MLLE Domain of PABPC1.","date":"2020","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/32517187","citation_count":10,"is_preprint":false},{"pmid":"37356415","id":"PMC_37356415","title":"LARP4A and LARP4B in cancer: The new kids on the block.","date":"2023","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/37356415","citation_count":8,"is_preprint":false},{"pmid":"29462618","id":"PMC_29462618","title":"Overexpression of Larp4B downregulates dMyc and reduces cell and organ sizes in Drosophila.","date":"2018","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/29462618","citation_count":4,"is_preprint":false},{"pmid":"39717893","id":"PMC_39717893","title":"Overexpression of lncRNA LINC00294 Induces Cell Cycle Arrest and Apoptosis in Colorectal Cancer by Regulating the miR-499a-5p/LARP4B Axis.","date":"2025","source":"Journal of biochemical and molecular toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/39717893","citation_count":4,"is_preprint":false},{"pmid":"41014504","id":"PMC_41014504","title":"LARP4B inhibits ferroptosis and accelerates the progression of pancreatic cancer by activating WNK1-induced NRF2/GCH1/BH4 pathway.","date":"2025","source":"Integrative biology : quantitative biosciences from nano to macro","url":"https://pubmed.ncbi.nlm.nih.gov/41014504","citation_count":2,"is_preprint":false},{"pmid":"37956874","id":"PMC_37956874","title":"CircRNA Larp4b/miR-298-5p/Mef2c Regulates Cardiac Hypertrophy Induced by Angiotensin II.","date":"2023","source":"International journal of sports medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37956874","citation_count":2,"is_preprint":false},{"pmid":"23815932","id":"PMC_23815932","title":"[Knockdown of Larp4b in Lin(-) cells does not affect the colony forming ability of mouse hematopoietic cells].","date":"2013","source":"Zhongguo shi yan xue ye xue za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/23815932","citation_count":1,"is_preprint":false},{"pmid":"41467969","id":"PMC_41467969","title":"microRNA-1258 suppresses breast cancer progression by targeting LARP4B.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41467969","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.11.01.621267","title":"The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation","date":"2024-11-01","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.01.621267","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9229,"output_tokens":2309,"usd":0.031161,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9378,"output_tokens":3062,"usd":0.06172,"stage2_stop_reason":"end_turn"},"total_usd":0.092881,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"LARP4B binds to 3' UTRs of a distinct set of cellular mRNAs, with a defined AU-rich binding motif identified by PAR-CLIP and in vitro binding assays; reduction of LARP4B destabilizes these mRNA targets and reduces their translation.\",\n      \"method\": \"PAR-CLIP transcriptome-wide analysis, biocomputational motif analysis, in vitro binding assays, knockdown with mRNA stability and proteome readout\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — PAR-CLIP (transcriptome-wide), in vitro binding assays, and functional knockdown with two orthogonal readouts (mRNA stability and translation), multiple methods in one study\",\n      \"pmids\": [\"26001795\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The La module (LA motif + adjacent RRM) of LARP4B is required for its growth-suppressive activity and directly associates with BAX mRNA, as shown by mutagenesis and RNA association assays in glioma cells.\",\n      \"method\": \"La module deletion mutagenesis, RNA immunoprecipitation/association assay, overexpression in glioma cell lines with proliferation/apoptosis readout\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mutagenesis plus mRNA association, single lab with two orthogonal methods\",\n      \"pmids\": [\"26933087\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The crystal structure of the variant PAM2w motif in the N-terminal region of LARP4B bound to the MLLE domain of PABPC1 revealed a new mode of PAM2–MLLE interaction; mutational studies in vitro and in vivo confirmed the structural contacts are required for binding.\",\n      \"method\": \"X-ray crystallography, mutational analysis in vitro and in vivo\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with mutational validation both in vitro and in vivo, orthogonal methods in one rigorous study\",\n      \"pmids\": [\"32517187\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In Drosophila, overexpression of Larp4B reduces cell and organ size; this effect requires the LA motif and RRM RNA-binding domains and is mediated by downregulation of dMyc protein levels. Loss-of-function mutation of larp4B increases dMyc protein. Genetic epistasis showed that dMyc overexpression suppresses the larp4B-overexpression phenotype.\",\n      \"method\": \"Transgenic overexpression, deletion mutant transgenes, genetic epistasis (dMyc suppressor), Western blot for dMyc protein\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis plus domain mutagenesis and protein level readout, single lab\",\n      \"pmids\": [\"29462618\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LARP4B binds to SPINK1 mRNA via its La motif and stabilizes it, thereby activating the SPINK1–EGFR signaling pathway to promote HCC progression. LARP4B expression is upregulated in HCC via METTL3-mediated m6A modification recognized by IGF2BP3.\",\n      \"method\": \"RNA immunoprecipitation sequencing, RIP-seq, RNA pulldown, gain- and loss-of-function assays, in vivo xenograft, EGFR pathway readout\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP-seq plus functional assays, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"38693111\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LARP4B binds to WNK1 mRNA and promotes its stability; stabilized WNK1 competitively binds the Kelch domain of Keap1, promoting NRF2 nuclear translocation and activation of the NRF2/GCH1/BH4 pathway, thereby inhibiting ferroptosis in pancreatic cancer cells.\",\n      \"method\": \"RNA binding/RIP assay for WNK1 mRNA, NRF2 nuclear translocation assay, NRF2 inhibitor (ML385) rescue, ROS/MDA/GSH/SOD measurements, in vivo xenograft\",\n      \"journal\": \"Integrative biology : quantitative biosciences from nano to macro\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP plus pharmacological rescue and multiple orthogonal functional readouts, single lab\",\n      \"pmids\": [\"41014504\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LARP4B (and LARP4) conserved region-2 (CR2), specifically positions 615–625, directly binds RACK1 region 200–317 (a ribosome-associated protein); CR2 mutations decrease LARP4B association with RACK1 and ribosomes, impair stabilization of AU-rich element (ARE)-containing mRNAs, and reduce translation efficiency of ARE-containing reporters. AlphaFold2-multimer predicted high-confidence interaction of CR2 with RACK1 propellers 5–6, consistent with experimental results.\",\n      \"method\": \"Yeast two-hybrid domain mapping, co-immunoprecipitation, polysome profiling, β-globin-ARE mRNA reporter assay, nanoLuc-ARE luciferase assay, CR2 mutagenesis, AlphaFold2-multimer structural prediction\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid plus Co-IP, ribosome association, and reporter translation assays with mutagenesis; preprint, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"bio_10.1101_2024.11.01.621267\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LARP4B (but not LARP4A) specifically regulates cell cycle progression in osteosarcoma and prostate cancer cells, modulating key cell cycle proteins including Cyclins B1 and E2, Aurora B, and E2F1, as determined by transcriptomic profiling and high-content multiparametric analyses following LARP4B depletion.\",\n      \"method\": \"siRNA/shRNA depletion, transcriptomic profiling, high-content multiparametric imaging analysis, xenograft models\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with defined cellular phenotype and transcriptomic profiling, single lab, two orthogonal readouts\",\n      \"pmids\": [\"38532886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Knockdown of Larp4b in mouse Lin(-) hematopoietic progenitor cells did not affect colony-forming ability, apoptosis, or cell cycle in vitro (negative result).\",\n      \"method\": \"Lentiviral shRNA knockdown in mouse Lin(-) cells, colony forming cell assay, AnnexinV/PI staining, RT-PCR\",\n      \"journal\": \"Zhongguo shi yan xue ye xue za zhi\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single method (colony assay), single lab, negative result only\",\n      \"pmids\": [\"23815932\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LARP4B is an RNA-binding protein that uses its La module (LA motif + RRM) to bind AU-rich sequences in the 3' UTRs of target mRNAs, stabilizing them and promoting their translation; it physically interacts with PABPC1 via a variant PAM2w motif (crystal structure resolved) and with ribosome-associated RACK1 via a conserved region-2 (CR2), the latter interaction promoting translational efficiency especially of ARE-containing mRNAs; LARP4B also stabilizes specific oncogenic mRNAs (e.g., SPINK1, WNK1) to activate downstream signaling pathways, and its RNA-binding domains are required for its roles in regulating cell growth, cell cycle, and dMyc levels.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LARP4B is an RNA-binding protein that selects a defined set of cellular mRNAs through their 3' UTRs and acts post-transcriptionally to stabilize them and promote their translation [#0]. Target recognition is mediated by its La module (the LA motif plus adjacent RRM), which binds an AU-rich sequence motif and is required both for direct mRNA association and for LARP4B's effects on cell growth [#0, #1]. LARP4B is integrated into the translational machinery through two protein contacts: its N-terminal variant PAM2w motif engages the MLLE domain of the poly(A)-binding protein PABPC1 in a structurally distinct PAM2–MLLE mode [#2], and its conserved region-2 directly binds the ribosome-associated protein RACK1, an interaction that enhances stabilization and translation efficiency of ARE-containing mRNAs [#6]. Through these activities LARP4B controls cell and organ size and cell cycle progression: in Drosophila its growth-suppressive effect depends on the LA motif and RRM and operates by lowering dMyc protein levels [#3], while in human tumor cells its depletion deregulates cell-cycle regulators including Cyclins B1 and E2, Aurora B, and E2F1 [#7]. In cancer contexts LARP4B stabilizes specific oncogenic transcripts—SPINK1 to drive SPINK1–EGFR signaling in hepatocellular carcinoma and WNK1 to engage the Keap1/NRF2/GCH1/BH4 axis and suppress ferroptosis in pancreatic cancer—linking its mRNA-stabilizing function to downstream signaling outputs [#4, #5].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"An early loss-of-function test asked whether LARP4B is required for hematopoietic progenitor function, establishing a context-dependent rather than universal cellular requirement.\",\n      \"evidence\": \"Lentiviral shRNA knockdown in mouse Lin(-) progenitor cells with colony-forming, apoptosis, and cell-cycle readouts\",\n      \"pmids\": [\"23815932\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Negative result from a single colony-forming assay; does not exclude roles in other cell types or molecular functions\",\n        \"No molecular target or binding activity tested\",\n        \"No protein-level or stability readout\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined LARP4B's core molecular activity by identifying its transcriptome-wide mRNA targets and showing it stabilizes them and promotes their translation, establishing it as a 3' UTR-binding post-transcriptional regulator.\",\n      \"evidence\": \"PAR-CLIP transcriptome-wide mapping, motif analysis, in vitro binding, and knockdown with mRNA-stability and proteome readouts\",\n      \"pmids\": [\"26001795\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Did not resolve which protein partners couple binding to stabilization/translation\",\n        \"AU-rich motif defined but structural basis of recognition not determined\"\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Localized the RNA-binding and growth-regulatory function to the La module, linking a specific domain to direct mRNA association and a cellular phenotype.\",\n      \"evidence\": \"La module deletion mutagenesis and RNA association assays with proliferation/apoptosis readout in glioma cells\",\n      \"pmids\": [\"26933087\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single target mRNA (BAX) tested for association\",\n        \"Single lab; mechanism connecting La-module binding to growth suppression not fully resolved\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Provided in vivo genetic evidence that LARP4B controls organismal growth, defining dMyc as a key downstream effector and confirming the RNA-binding domains are required.\",\n      \"evidence\": \"Drosophila transgenic overexpression and loss-of-function, domain-deletion transgenes, dMyc genetic epistasis, and Western blot\",\n      \"pmids\": [\"29462618\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether dMyc regulation is direct (mRNA binding) versus indirect not resolved\",\n        \"Mammalian conservation of the dMyc/MYC axis not tested here\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Resolved the structural basis of the LARP4B–PABPC1 interaction, revealing a variant PAM2w–MLLE binding mode and validating the contacts functionally.\",\n      \"evidence\": \"X-ray crystallography of the PAM2w–MLLE complex with mutational analysis in vitro and in vivo\",\n      \"pmids\": [\"32517187\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Functional consequence of disrupting PABPC1 binding on specific mRNA targets not detailed\",\n        \"How this contact integrates with La-module mRNA binding not addressed\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified RACK1 as a direct ribosome-associated partner via conserved region-2, mechanistically coupling LARP4B to the ribosome and to ARE-mRNA stabilization and translation.\",\n      \"evidence\": \"Yeast two-hybrid domain mapping, Co-IP, polysome profiling, ARE reporter assays, CR2 mutagenesis, and AlphaFold2-multimer prediction (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.11.01.621267\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Preprint, single lab; structural prediction not experimentally validated\",\n        \"Reciprocal endogenous interaction and stoichiometry on ribosomes not established\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established LARP4B as a paralog-specific cell-cycle regulator, distinguishing its function from LARP4A and identifying affected cell-cycle proteins.\",\n      \"evidence\": \"siRNA/shRNA depletion with transcriptomic profiling, high-content multiparametric imaging, and xenografts in osteosarcoma and prostate cancer cells\",\n      \"pmids\": [\"38532886\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether cell-cycle gene changes are direct mRNA targets versus secondary not resolved\",\n        \"Single lab\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected LARP4B's mRNA-stabilizing activity to defined oncogenic signaling outputs by showing it stabilizes specific transcripts to drive disease-relevant pathways.\",\n      \"evidence\": \"RIP-seq/RIP, RNA pulldown, gain/loss-of-function, pathway readouts (SPINK1–EGFR; WNK1–Keap1/NRF2/GCH1/BH4 ferroptosis), and xenografts in HCC and pancreatic cancer\",\n      \"pmids\": [\"38693111\", \"41014504\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Each axis shown in a single tumor context by a single lab\",\n        \"Generality of these targets across tissues not established\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the La-module mRNA recognition, PABPC1 binding, and RACK1/ribosome coupling are integrated into a unified mechanism that selects which target mRNAs are stabilized versus translationally enhanced in a given cell type remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No integrated structural/biochemical model linking all three binding activities on a single mRNP\",\n        \"Rules governing target selectivity across tissues not defined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 4, 5, 6]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [3, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PABPC1\",\n      \"RACK1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":5,"faith_pct":100.0}}