{"gene":"DDX24","run_date":"2026-04-28T17:46:02","timeline":{"discoveries":[{"year":2000,"finding":"DDX24 was cloned and characterized as a DEAD-box protein with all conserved DEAD-box motifs, showing ubiquitous expression across human tissues and mapping to chromosome 14q32; the gene spans ~30 kb with at least nine exons.","method":"cDNA cloning, Northern blot, radiation hybrid mapping, genomic sequence comparison","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 — direct cloning and mapping, but purely characterization without functional mechanistic assay","pmids":["10936056"],"is_preprint":false},{"year":2008,"finding":"DDX24 knockdown inhibits HIV-1 RNA packaging and viral infectivity specifically in the context of Rev/RRE-dependent nuclear export; DDX24 interacts with the HIV-1 Rev protein, indicating it acts at an early phase of viral RNA metabolism prior to nuclear export.","method":"siRNA knockdown, HIV-1 RNA packaging assay, co-immunoprecipitation (DDX24–Rev interaction), CTE vs. RRE comparison","journal":"Virology","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP plus functional packaging assay with mechanistic comparison, single lab","pmids":["18289627"],"is_preprint":false},{"year":2013,"finding":"DDX24 negatively regulates RIG-I-like receptor (RLR)-mediated innate immune signaling by associating with adaptor proteins FADD and RIP1, preferentially impeding IRF7 activity to suppress type I IFN production; DDX24 preferentially binds RNA rather than DNA.","method":"DDX24 overexpression/knockdown in reporter assays, co-immunoprecipitation (DDX24–FADD and DDX24–RIP1), RNA vs. DNA binding assays, DDX24 loss-of-function (embryonic lethality model)","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, functional reporter, nucleic acid binding), moderately replicated context","pmids":["24204270"],"is_preprint":false},{"year":2014,"finding":"MDM2 interacts with the central region of DDX24 and mediates its nonproteolytic polyubiquitylation (both in vitro and in vivo); this ubiquitylation promotes DDX24 association with preribosomal ribonucleoprotein (pre-rRNP) processing complexes required for early pre-rRNA processing steps; DDX24 depletion impairs pre-rRNA processing, abrogates MDM2 function, and leads to p53 stabilization.","method":"Co-immunoprecipitation (DDX24–MDM2), in vitro and in vivo ubiquitylation assays, pre-rRNA processing assays, DDX24 knockdown with p53 stabilization readout","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro ubiquitylation reconstitution plus in vivo Co-IP, multiple functional readouts in single study","pmids":["24980433"],"is_preprint":false},{"year":2015,"finding":"DDX24 interacts with p300, suppressing p300-mediated acetylation of p53; DDX24 overexpression inhibits the p300–p53 interaction, while DDX24 knockdown increases endogenous p53 acetylation, activates p21 and PUMA expression, and induces cell cycle arrest and senescence in a p53-dependent manner.","method":"Co-immunoprecipitation (DDX24–p300, p300–p53), acetylation assays, siRNA knockdown, cell cycle and senescence assays","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP plus acetylation assay plus p53-dependent rescue, multiple orthogonal methods","pmids":["25867071"],"is_preprint":false},{"year":2019,"finding":"DDX24 mutations (including K11E and E271K in the ATP-binding domain) are associated with vascular malformations; DDX24 knockdown in endothelial cells elevates migration and tube formation, establishing a functional role in endothelial cell behavior.","method":"Genetic mutation analysis, structural modeling, siRNA knockdown, endothelial cell migration and tube formation assays, transcriptomic analysis","journal":"Hepatology","confidence":"Medium","confidence_rationale":"Tier 2 — knockdown with defined cellular phenotype, genetic link; structural modeling is computational","pmids":["30063812"],"is_preprint":false},{"year":2022,"finding":"LINC02551 acts as a molecular adaptor that blocks the interaction between DDX24 and the E3 ubiquitin ligase TRIM27, thereby decreasing ubiquitination and proteasomal degradation of DDX24 and promoting HCC progression; ALKBH5-mediated m6A demethylation of LINC02551 destabilizes LINC02551 and consequently reduces DDX24 protein.","method":"Co-immunoprecipitation (DDX24–TRIM27), ubiquitination assay, m6A modification analysis, knockdown/overexpression functional assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus ubiquitination assay plus functional rescue, single lab","pmids":["36335087"],"is_preprint":false},{"year":2022,"finding":"DDX24 binds the LAMB1 mRNA (nt 618–624) and increases its stability in a manner dependent on interaction between nucleolin and the C-terminal region of DDX24, promoting HCC migration and proliferation.","method":"RNA immunoprecipitation, mRNA stability assay, Co-immunoprecipitation (DDX24–nucleolin), overexpression/knockdown with migration/proliferation readouts","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — RIP plus mRNA stability plus protein interaction, single lab with multiple orthogonal methods","pmids":["35763670"],"is_preprint":false},{"year":2022,"finding":"DDX24 and DDX49 bind predominantly to immediate-early and early KSHV mRNAs (shown by RNA immunoprecipitation followed by next-generation sequencing) and exert antiviral activity by suppressing lytic viral transcription and genome replication when overexpressed in BCBL-1 cells.","method":"RNA immunoprecipitation-seq (tagged DDX24), overexpression in BCBL-1 cells, viral gene expression and replication assays, RNA pulldown with candidate transcripts","journal":"Viruses","confidence":"Medium","confidence_rationale":"Tier 2 — RIP-seq plus functional antiviral assay, single lab","pmids":["36298642"],"is_preprint":false},{"year":2022,"finding":"DDX24 interacts with RPL5 and promotes its ubiquitination and destabilization in NSCLC cells, enhancing cancer cell migration and invasion.","method":"Co-immunoprecipitation followed by mass spectrometry, protein stability assay, ubiquitination assay, knockdown/overexpression migration and invasion assays","journal":"Cancer medicine","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP/MS plus ubiquitination assay, single lab","pmids":["35864588"],"is_preprint":false},{"year":2022,"finding":"Loss-of-function mutations K11E and E271K in DDX24 reduce nucleolar number and cell proliferation, consistent with DDX24's role as an oncogenic factor in the nucleolus; these mutations decrease tumor formation in mouse xenograft models and alter immune-related signaling pathways.","method":"Stable cell line expression of WT and mutant DDX24, immunofluorescence (nucleoli counting), proliferation/colony assays, xenograft mouse models, transcriptome sequencing","journal":"International journal of medical sciences","confidence":"Medium","confidence_rationale":"Tier 2 — multiple functional assays with defined mutations in vivo and in vitro","pmids":["35370459"],"is_preprint":false},{"year":2023,"finding":"DDX24 mutation E271K causes DDX24 to partition less into nucleoli; DDX24 directly associates with NPM1 and regulates its liquid-liquid phase separation behavior as a client in the nucleolar granular component; mutation or knockdown of DDX24 disrupts nucleolar homeostasis, impairs ribosome biogenesis, and elevates endothelial cell migration and tube formation.","method":"In vitro biomolecular condensate assay, Co-immunoprecipitation (DDX24–NPM1), immunofluorescence in patient tissues and ECs, knockdown and mutation functional assays (migration, tube formation, ribosome biogenesis)","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro phase separation plus Co-IP plus patient tissue validation, single lab with multiple orthogonal methods","pmids":["37705750"],"is_preprint":false},{"year":2023,"finding":"DDX24 binds FANCA mRNA and stabilizes it; DDX24 loss leads to decreased FANCA, increased DNA damage, and cell cycle arrest in vascular smooth muscle cells; overexpression of FANCA rescues the DDX24-deficiency phenotype; VSMC-specific Ddx24 knockout mice die before E13.5 with defective vessel formation.","method":"RNA immunoprecipitation with qRT-PCR, RNA stability assay (RNA pulldown), VSMC-specific Cre-loxP knockout mice, flow cytometry, cell proliferation assay, rescue with FANCA overexpression","journal":"Arteriosclerosis, thrombosis, and vascular biology","confidence":"High","confidence_rationale":"Tier 1–2 — RIP, RNA pulldown, in vivo genetic knockout with epistatic rescue, multiple orthogonal methods","pmids":["37470182"],"is_preprint":false},{"year":2023,"finding":"DDX24 binds HK1 mRNA and positively regulates HK1 expression at the transcriptional level, promoting glycolysis (glucose uptake, lactate production) and tumor cell proliferation, migration, and invasion in gastric cancer.","method":"RNA binding assay (DDX24–HK1 mRNA), knockdown/overexpression with glycolysis readouts (glucose uptake, lactate), proliferation and migration assays","journal":"Cellular signalling","confidence":"Low","confidence_rationale":"Tier 3 — single lab, mRNA binding assay with functional follow-up, limited mechanistic detail","pmids":["38043669"],"is_preprint":false},{"year":2024,"finding":"Endothelium-targeted Ddx24 conditional knockout (Cdh5-Cre system) in mice leads to elevated endothelial migration and tube formation, vascular hyper-permeability, and exacerbated ConA-induced hepatitis with elevated TNF-α and IFN-γ; mass spectrometry identified downregulation of vascular integrity-associated proteins.","method":"CRISPR/Cas9-mediated Cre-loxP conditional knockout, endothelial cell migration and tube formation assays, in vivo ConA hepatitis model, mass spectrometry of liver tissue proteins","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2 — conditional knockout with defined in vivo phenotype and MS-based protein profiling","pmids":["38354508"],"is_preprint":false},{"year":2025,"finding":"DDX24 regulates alternative splicing of IKBKG pre-mRNA; DDX24 directly binds IKBKG pre-mRNA, and DDX24 ablation stimulates generation of the long IKBKG isoform, which activates NF-κB signaling, induces BECN1 transcription, and promotes autophagy to suppress lung cancer growth.","method":"Mass spectrometry (splicing interactome), RNA sequencing (alternative splicing), Co-immunoprecipitation, luciferase reporter assays, direct mRNA binding, xenograft tumor models, functional rescue with long IKBKG isoform","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods (MS, RNAseq, Co-IP, reporter, rescue), single lab","pmids":["39897555"],"is_preprint":false},{"year":2025,"finding":"DDX24 deficiency in zebrafish endothelium enhances VEGFR2 expression by direct binding to its mRNA in non-brain endothelial cells, causing intersegmental vessel hyperbranching; in brain endothelial cells, DDX24 deficiency suppresses GPR124/RECK-mediated Wnt signaling; pharmacological rescue of both pathways in temporal sequence corrects the vascular phenotypes.","method":"Zebrafish ddx24 morpholino/mutant, direct mRNA binding assay (VEGFR2 mRNA), spatial transcriptome analysis, pharmacological epistasis, endothelial cell-type-specific dissection","journal":"PNAS","confidence":"High","confidence_rationale":"Tier 1–2 — direct mRNA binding plus in vivo genetic model plus pharmacological epistasis rescue, multiple orthogonal methods","pmids":["40339127"],"is_preprint":false},{"year":2025,"finding":"DDX24 binds PPFIA4 mRNA and enhances its stability; DDX24 knockdown reduces PPFIA4, causing occludin phosphorylation and mitochondrial dysfunction in cerebral microvascular endothelial cells; endothelial-specific Ddx24 KO mice show increased BBB permeability and learning/memory deficits; NADPH oxidase inhibition rescues these phenotypes.","method":"Endothelial-specific Ddx24 conditional knockout mice, RNA binding/stability assay (DDX24–PPFIA4 mRNA), Co-IP, occludin phosphorylation assay, mitochondrial function assay, NADPH oxidase inhibitor rescue, behavioral tests","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1–2 — conditional KO with defined in vivo phenotype, mRNA binding/stability, pharmacological rescue, multiple orthogonal methods","pmids":["41105514"],"is_preprint":false},{"year":2025,"finding":"DDX24 regulates HO-1 gene transcription (not mRNA stability) under oxidative stress, likely acting at the HO-1 promoter and enhancer E1 region; DDX24 depletion reduces HO-1 expression, cell viability, and anti-apoptotic/anti-oxidative capacity.","method":"RNA sequencing (DDX24-depleted vs. overexpressing cells), HO-1 promoter/enhancer reporter assays, mRNA stability assay, knockdown/overexpression with apoptosis and oxidative stress readouts","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2 — reporter assay distinguishes transcriptional vs. post-transcriptional mechanism, plus mRNA stability assay, single lab","pmids":["40847746"],"is_preprint":false},{"year":2026,"finding":"DDX24 directly binds specific endothelial mRNAs (including CLEC14A and ERG) identified by iCLIP-seq, and promotes their decay through interaction with the CCR4-NOT deadenylase complex, thereby regulating angiogenesis.","method":"Infrared cross-linking immunoprecipitation sequencing (iCLIP-seq), Co-immunoprecipitation (DDX24–CCR4-NOT complex), mRNA decay assays, endothelial functional assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 — iCLIP-seq for direct binding plus Co-IP of CCR4-NOT complex plus mRNA decay assay, multiple orthogonal methods","pmids":["41728947"],"is_preprint":false}],"current_model":"DDX24 is a nucleolar DEAD-box RNA helicase that directly binds specific mRNAs to regulate their stability or splicing (e.g., LAMB1, FANCA, VEGFR2, PPFIA4, IKBKG), promotes CCR4-NOT-dependent mRNA decay in endothelial cells, undergoes MDM2-mediated nonproteolytic polyubiquitylation to facilitate pre-rRNA processing, interacts with p300 to suppress p53 acetylation and with FADD/RIP1 to attenuate IRF7-driven type I interferon responses, is subject to TRIM27-mediated ubiquitination and proteasomal degradation (counteracted by the lncRNA LINC02551), and plays essential roles in vascular development, ribosome biogenesis, innate immune regulation, and cancer cell proliferation and migration."},"narrative":{"teleology":[{"year":2000,"claim":"Identification of DDX24 as a conserved DEAD-box family member established it as a candidate RNA helicase, but its cellular function remained unknown.","evidence":"cDNA cloning, Northern blot, and radiation hybrid mapping in human tissues","pmids":["10936056"],"confidence":"Medium","gaps":["No enzymatic or functional assay performed","Helicase activity not demonstrated","No subcellular localization determined"]},{"year":2008,"claim":"Linking DDX24 to HIV-1 Rev-dependent RNA packaging provided the first functional evidence that DDX24 participates in nuclear RNA export and viral RNA metabolism.","evidence":"siRNA knockdown, HIV-1 RNA packaging assay, and Co-IP of DDX24–Rev interaction","pmids":["18289627"],"confidence":"Medium","gaps":["Whether DDX24 directly unwinds viral RNA structures not tested","Role in endogenous mRNA export not addressed","Single viral system"]},{"year":2013,"claim":"Discovery that DDX24 suppresses RLR-mediated type I interferon signaling through FADD/RIP1 interaction established it as a negative regulator of innate immunity, revealing a non-canonical function beyond RNA metabolism.","evidence":"Overexpression/knockdown reporter assays, Co-IP of DDX24–FADD and DDX24–RIP1, RNA vs. DNA binding assays","pmids":["24204270"],"confidence":"High","gaps":["Precise mechanism of IRF7 inhibition not defined at the structural level","Whether helicase activity is required for immune suppression not tested"]},{"year":2014,"claim":"Demonstrating that MDM2 mediates nonproteolytic polyubiquitylation of DDX24 to promote its association with pre-rRNP complexes resolved how DDX24 enters the ribosome biogenesis pathway and connected ribosomal stress to p53 stabilization.","evidence":"In vitro and in vivo ubiquitylation assays, Co-IP of DDX24–MDM2, pre-rRNA processing assays, p53 stabilization readout","pmids":["24980433"],"confidence":"High","gaps":["Which specific pre-rRNA processing step DDX24 catalyzes remains unclear","Ubiquitylation sites on DDX24 not mapped","Direct helicase activity on pre-rRNA not shown"]},{"year":2015,"claim":"Finding that DDX24 inhibits p300-mediated p53 acetylation explained how DDX24 depletion activates p53 target genes (p21, PUMA), linking DDX24 to cell cycle control and senescence independently of ribosomal stress.","evidence":"Co-IP of DDX24–p300 and p300–p53, acetylation assays, siRNA knockdown with cell cycle and senescence readouts","pmids":["25867071"],"confidence":"High","gaps":["Whether the DDX24–p300 interaction requires RNA binding or helicase activity is unknown","Relationship between nucleolar and p300-mediated p53 regulation not dissected"]},{"year":2019,"claim":"Identification of DDX24 mutations (K11E, E271K) in patients with vascular malformations provided the first genetic evidence that DDX24 loss-of-function causes human vascular disease, linking its molecular functions to endothelial biology.","evidence":"Genetic mutation analysis, siRNA knockdown in endothelial cells with migration and tube formation assays","pmids":["30063812"],"confidence":"Medium","gaps":["Causal mechanism by which mutations cause vascular malformations not fully defined","Patient cohort limited"]},{"year":2022,"claim":"Multiple studies in 2022 established DDX24 as a direct mRNA-binding protein that stabilizes LAMB1 mRNA (via nucleolin interaction), promotes RPL5 ubiquitination and degradation, and suppresses KSHV lytic replication, broadening its role to post-transcriptional regulation and cancer cell proliferation.","evidence":"RNA immunoprecipitation, mRNA stability assays, Co-IP/MS (DDX24–RPL5, DDX24–nucleolin), RIP-seq in KSHV-infected cells, knockdown/overexpression with functional readouts","pmids":["35763670","35864588","36298642"],"confidence":"Medium","gaps":["Whether mRNA stabilization requires helicase activity is untested","RPL5 ubiquitination mechanism (direct vs. adaptor) unclear","KSHV antiviral mechanism is descriptive"]},{"year":2022,"claim":"Demonstration that TRIM27 ubiquitylates DDX24 for proteasomal degradation and that LINC02551 blocks this interaction revealed a regulatory axis controlling DDX24 protein levels in hepatocellular carcinoma, connecting m6A RNA modification to DDX24 abundance.","evidence":"Co-IP of DDX24–TRIM27, ubiquitination assays, m6A modification analysis, functional rescue","pmids":["36335087"],"confidence":"Medium","gaps":["TRIM27 ubiquitination sites on DDX24 not mapped","Single cancer type studied","LINC02551 structural basis for blocking TRIM27 unknown"]},{"year":2023,"claim":"Showing that DDX24 associates with NPM1 and modulates nucleolar liquid–liquid phase separation explained how DDX24 mutations disrupt nucleolar organization and ribosome biogenesis, connecting phase behavior to the vascular phenotype.","evidence":"In vitro biomolecular condensate assay, Co-IP of DDX24–NPM1, immunofluorescence in patient tissues, knockdown/mutation functional assays","pmids":["37705750"],"confidence":"Medium","gaps":["Whether DDX24 helicase activity drives phase separation partitioning not tested","Contribution of phase separation vs. enzymatic activity to ribosome biogenesis not separated"]},{"year":2023,"claim":"Conditional VSMC-specific Ddx24 knockout causing embryonic lethality before E13.5 with defective vessel formation, rescued by FANCA overexpression, established DDX24-dependent FANCA mRNA stabilization as essential for vascular smooth muscle cell survival and vessel integrity.","evidence":"VSMC-specific Cre-loxP knockout mice, RNA immunoprecipitation, mRNA stability assay, FANCA rescue","pmids":["37470182"],"confidence":"High","gaps":["DDX24 binding site on FANCA mRNA not mapped at nucleotide resolution","Whether other mRNA targets contribute to the VSMC lethal phenotype not excluded"]},{"year":2025,"claim":"Several 2025 studies revealed DDX24 as a versatile mRNA regulator in the vasculature: it directly binds VEGFR2 mRNA to limit angiogenic sprouting in zebrafish, stabilizes PPFIA4 mRNA to maintain blood-brain barrier integrity, and regulates IKBKG pre-mRNA splicing to control NF-κB-driven autophagy in lung cancer.","evidence":"Zebrafish morpholino/mutant with pharmacological epistasis, endothelial-specific Ddx24 KO mice with BBB permeability and behavioral tests, RNA-seq-based alternative splicing analysis with functional rescue in xenografts","pmids":["40339127","41105514","39897555"],"confidence":"High","gaps":["Structural basis for DDX24 target mRNA selectivity not resolved","Whether splicing regulation is direct unwinding or scaffolding is unclear","Brain vs. non-brain endothelial target specificity mechanism unknown"]},{"year":2025,"claim":"Identification of DDX24 as a transcriptional regulator of HO-1 under oxidative stress, acting at the promoter/enhancer rather than on mRNA stability, expanded its functional repertoire beyond post-transcriptional regulation.","evidence":"HO-1 promoter/enhancer reporter assays, mRNA stability assay ruling out post-transcriptional effect, knockdown/overexpression with oxidative stress readouts","pmids":["40847746"],"confidence":"Medium","gaps":["Whether DDX24 binds chromatin directly or acts through a transcription factor complex unknown","Mechanism distinguishing transcriptional from post-transcriptional target selection unclear"]},{"year":2026,"claim":"Transcriptome-wide iCLIP-seq mapping of DDX24 binding sites coupled with demonstration of CCR4-NOT complex interaction established that DDX24 recruits the deadenylase machinery to specific endothelial mRNAs to promote their decay, providing a unifying mechanism for its mRNA-destabilizing activities.","evidence":"iCLIP-seq for direct binding, Co-IP of DDX24–CCR4-NOT complex, mRNA decay assays in endothelial cells","pmids":["41728947"],"confidence":"High","gaps":["Whether DDX24 helicase activity is required for CCR4-NOT recruitment not tested","How DDX24 distinguishes mRNAs it stabilizes from those it promotes for decay is unresolved"]},{"year":null,"claim":"A central unresolved question is how DDX24 selects between stabilizing and destabilizing mRNA targets, and whether its enzymatic helicase activity—as opposed to scaffolding—is required for each of its diverse functions in ribosome biogenesis, mRNA regulation, innate immunity, and transcription.","evidence":"","pmids":[],"confidence":"High","gaps":["No crystal or cryo-EM structure of DDX24 alone or in complex","Helicase activity has never been directly measured in vitro on any substrate","Selectivity rules for mRNA stabilization vs. CCR4-NOT-dependent decay are unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[2,7,8,12,15,16,17,19]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[7,12,15,17,19]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,4,15]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[18]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[3,10,11]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,3,4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[7,12,15,16,17,19]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[3,9,11]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[2,14]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[18]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[5,12,16]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[15]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[3,11]}],"complexes":["CCR4-NOT deadenylase complex"],"partners":["MDM2","NPM1","TRIM27","FADD","RIP1","TP53","EP300","NCL"],"other_free_text":[]},"mechanistic_narrative":"DDX24 is a DEAD-box RNA helicase that functions as a multifaceted post-transcriptional and transcriptional regulator essential for ribosome biogenesis, vascular development, and innate immune homeostasis. DDX24 directly binds specific mRNAs—including LAMB1, FANCA, VEGFR2, PPFIA4, and IKBKG—to regulate their stability or alternative splicing, and promotes CCR4-NOT-dependent mRNA decay of endothelial transcripts such as CLEC14A and ERG to control angiogenesis [PMID:41728947, PMID:37470182, PMID:40339127, PMID:39897555]. In the nucleolus, MDM2-mediated nonproteolytic polyubiquitylation of DDX24 facilitates its association with pre-rRNP complexes required for pre-rRNA processing, and DDX24 regulates nucleolar organization through NPM1-dependent liquid–liquid phase separation [PMID:24980433, PMID:37705750]. DDX24 additionally suppresses p53 activation by inhibiting p300-mediated p53 acetylation, attenuates RLR-mediated type I interferon responses by associating with FADD and RIP1, and is itself subject to TRIM27-mediated proteasomal degradation counteracted by the lncRNA LINC02551 [PMID:25867071, PMID:24204270, PMID:36335087]."},"prefetch_data":{"uniprot":{"accession":"Q9GZR7","full_name":"ATP-dependent RNA helicase DDX24","aliases":["DEAD box protein 24"],"length_aa":859,"mass_kda":96.3,"function":"ATP-dependent RNA helicase that plays a role in various aspects of RNA metabolism including pre-mRNA splicing and is thereby involved in different biological processes such as cell cycle regulation or innate immunity (PubMed:24204270, PubMed:24980433). Plays an inhibitory role in TP53 transcriptional activity and subsequently in TP53 controlled cell growth arrest and senescence by inhibiting its EP300 mediated acetylation (PubMed:25867071). Negatively regulates cytosolic RNA-mediated innate immune signaling at least in part by affecting RIPK1/IRF7 interactions. Alternatively, possesses antiviral activity by recognizing gammaherpesvirus transcripts in the context of lytic reactivation (PubMed:36298642). Plays an essential role in cell cycle regulation in vascular smooth muscle cells by interacting with and regulating FANCA (Fanconi anemia complementation group A) mRNA (By similarity) (Microbial infection) Plays a positive role in HIV-1 infection by promoting Rev-dependent nuclear export of viral RNAs and their packaging into virus particles (PubMed:24204270)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9GZR7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/DDX24","classification":"Common Essential","n_dependent_lines":1152,"n_total_lines":1208,"dependency_fraction":0.9536423841059603},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CSNK2B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/DDX24","total_profiled":1310},"omim":[{"mim_id":"606181","title":"DEAD-BOX HELICASE 24; DDX24","url":"https://www.omim.org/entry/606181"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DDX24"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q9GZR7","domains":[{"cath_id":"3.40.50.300","chopping":"185-263_385-520_528-555","consensus_level":"medium","plddt":83.4409,"start":185,"end":555},{"cath_id":"3.40.50.300","chopping":"564-715","consensus_level":"high","plddt":88.8796,"start":564,"end":715},{"cath_id":"1.20.58","chopping":"727-798","consensus_level":"high","plddt":86.5883,"start":727,"end":798}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZR7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZR7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZR7-F1-predicted_aligned_error_v6.png","plddt_mean":64.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DDX24","jax_strain_url":"https://www.jax.org/strain/search?query=DDX24"},"sequence":{"accession":"Q9GZR7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9GZR7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9GZR7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZR7"}},"corpus_meta":[{"pmid":"24204270","id":"PMC_24204270","title":"DDX24 negatively regulates cytosolic RNA-mediated innate immune signaling.","date":"2013","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/24204270","citation_count":74,"is_preprint":false},{"pmid":"18289627","id":"PMC_18289627","title":"The requirement of the DEAD-box protein DDX24 for the packaging of human immunodeficiency virus type 1 RNA.","date":"2008","source":"Virology","url":"https://pubmed.ncbi.nlm.nih.gov/18289627","citation_count":51,"is_preprint":false},{"pmid":"25867071","id":"PMC_25867071","title":"Negative regulation of the p300-p53 interplay by DDX24.","date":"2015","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/25867071","citation_count":41,"is_preprint":false},{"pmid":"36335087","id":"PMC_36335087","title":"ALKBH5-mediated m6A modification of lincRNA LINC02551 enhances the stability of DDX24 to promote hepatocellular carcinoma growth and metastasis.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/36335087","citation_count":41,"is_preprint":false},{"pmid":"35763670","id":"PMC_35763670","title":"RNA Helicase DDX24 Stabilizes LAMB1 to Promote Hepatocellular Carcinoma Progression.","date":"2022","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/35763670","citation_count":28,"is_preprint":false},{"pmid":"24980433","id":"PMC_24980433","title":"MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-Box RNA helicase DDX24.","date":"2014","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/24980433","citation_count":19,"is_preprint":false},{"pmid":"30063812","id":"PMC_30063812","title":"DDX24 Mutations Associated With Malformations of Major Vessels to the Viscera.","date":"2019","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/30063812","citation_count":17,"is_preprint":false},{"pmid":"35864588","id":"PMC_35864588","title":"DDX24 promotes metastasis by regulating RPL5 in non-small cell lung cancer.","date":"2022","source":"Cancer medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35864588","citation_count":15,"is_preprint":false},{"pmid":"10936056","id":"PMC_10936056","title":"Cloning and characterization of human DDX24 and mouse Ddx24, two novel putative DEAD-Box proteins, and mapping DDX24 to human chromosome 14q32.","date":"2000","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/10936056","citation_count":14,"is_preprint":false},{"pmid":"37705750","id":"PMC_37705750","title":"DDX24 Mutation Alters NPM1 Phase Behavior and Disrupts Nucleolar Homeostasis in Vascular Malformations.","date":"2023","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37705750","citation_count":9,"is_preprint":false},{"pmid":"37470182","id":"PMC_37470182","title":"DDX24 Is Essential for Cell Cycle Regulation in Vascular Smooth Muscle Cells During Vascular Development via Binding to FANCA mRNA.","date":"2023","source":"Arteriosclerosis, thrombosis, and vascular biology","url":"https://pubmed.ncbi.nlm.nih.gov/37470182","citation_count":9,"is_preprint":false},{"pmid":"38043669","id":"PMC_38043669","title":"DDX24 promotes tumor progression by mediating hexokinase-1 induced glycolysis in gastric cancer.","date":"2023","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/38043669","citation_count":8,"is_preprint":false},{"pmid":"36298642","id":"PMC_36298642","title":"DExD/H Box Helicases DDX24 and DDX49 Inhibit Reactivation of Kaposi's Sarcoma Associated Herpesvirus by Interacting with Viral mRNAs.","date":"2022","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/36298642","citation_count":7,"is_preprint":false},{"pmid":"35523320","id":"PMC_35523320","title":"DDX24 is required for muscle fiber organization and the suppression of wound-induced Wnt activity necessary for pole re-establishment during planarian regeneration.","date":"2022","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/35523320","citation_count":6,"is_preprint":false},{"pmid":"40339127","id":"PMC_40339127","title":"DDX24 spatiotemporally orchestrates VEGF and Wnt signaling during developmental angiogenesis.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/40339127","citation_count":5,"is_preprint":false},{"pmid":"39897555","id":"PMC_39897555","title":"Loss of DDX24 inhibits lung cancer progression by stimulating IKBKG splicing-mediated autophagy.","date":"2025","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/39897555","citation_count":5,"is_preprint":false},{"pmid":"36310384","id":"PMC_36310384","title":"DDX24 regulates the chemosensitivity of hepatocellular carcinoma to sorafenib via mediating the expression of SNORA18.","date":"2022","source":"Cancer biology & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/36310384","citation_count":4,"is_preprint":false},{"pmid":"35370459","id":"PMC_35370459","title":"Loss-of-function Mutations K11E or E271K Lead to Novel Tumor Suppression, Implicate Nucleolar Helicase DDX24 Oncogenicity.","date":"2022","source":"International journal of medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35370459","citation_count":3,"is_preprint":false},{"pmid":"38354508","id":"PMC_38354508","title":"Endothelium-targeted Ddx24 conditional knockout exacerbates ConA-induced hepatitis in mice due to vascular hyper-permeability.","date":"2024","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/38354508","citation_count":1,"is_preprint":false},{"pmid":"40216172","id":"PMC_40216172","title":"DDX24 inhibits clear cell renal cell carcinoma progression by directly regulating AKR1B10.","date":"2025","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/40216172","citation_count":0,"is_preprint":false},{"pmid":"41105514","id":"PMC_41105514","title":"DEAD-box helicase DDX24 is essential for endothelial mitochondrial function to maintain the blood-brain barrier.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/41105514","citation_count":0,"is_preprint":false},{"pmid":"40847746","id":"PMC_40847746","title":"Anti-Apoptotic and Anti-Oxidative Effects of DDX24 Through HO-1 Transcriptional Regulation.","date":"2025","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/40847746","citation_count":0,"is_preprint":false},{"pmid":"41948606","id":"PMC_41948606","title":"Immunomodulatory Roles and Clinical Significance of GZMM and DDX24 in Sepsis: A Multiomics Integrative Analysis With Experimental Validation.","date":"2026","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/41948606","citation_count":0,"is_preprint":false},{"pmid":"41728947","id":"PMC_41728947","title":"DDX24 modulates angiogenesis by promoting CCR4-NOT complex-dependent mRNA decay.","date":"2026","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/41728947","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12349,"output_tokens":4794,"usd":0.054478},"stage2":{"model":"claude-opus-4-6","input_tokens":8343,"output_tokens":3605,"usd":0.19776},"total_usd":0.252238,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"DDX24 was cloned and characterized as a DEAD-box protein with all conserved DEAD-box motifs, showing ubiquitous expression across human tissues and mapping to chromosome 14q32; the gene spans ~30 kb with at least nine exons.\",\n      \"method\": \"cDNA cloning, Northern blot, radiation hybrid mapping, genomic sequence comparison\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct cloning and mapping, but purely characterization without functional mechanistic assay\",\n      \"pmids\": [\"10936056\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"DDX24 knockdown inhibits HIV-1 RNA packaging and viral infectivity specifically in the context of Rev/RRE-dependent nuclear export; DDX24 interacts with the HIV-1 Rev protein, indicating it acts at an early phase of viral RNA metabolism prior to nuclear export.\",\n      \"method\": \"siRNA knockdown, HIV-1 RNA packaging assay, co-immunoprecipitation (DDX24–Rev interaction), CTE vs. RRE comparison\",\n      \"journal\": \"Virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP plus functional packaging assay with mechanistic comparison, single lab\",\n      \"pmids\": [\"18289627\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DDX24 negatively regulates RIG-I-like receptor (RLR)-mediated innate immune signaling by associating with adaptor proteins FADD and RIP1, preferentially impeding IRF7 activity to suppress type I IFN production; DDX24 preferentially binds RNA rather than DNA.\",\n      \"method\": \"DDX24 overexpression/knockdown in reporter assays, co-immunoprecipitation (DDX24–FADD and DDX24–RIP1), RNA vs. DNA binding assays, DDX24 loss-of-function (embryonic lethality model)\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, functional reporter, nucleic acid binding), moderately replicated context\",\n      \"pmids\": [\"24204270\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"MDM2 interacts with the central region of DDX24 and mediates its nonproteolytic polyubiquitylation (both in vitro and in vivo); this ubiquitylation promotes DDX24 association with preribosomal ribonucleoprotein (pre-rRNP) processing complexes required for early pre-rRNA processing steps; DDX24 depletion impairs pre-rRNA processing, abrogates MDM2 function, and leads to p53 stabilization.\",\n      \"method\": \"Co-immunoprecipitation (DDX24–MDM2), in vitro and in vivo ubiquitylation assays, pre-rRNA processing assays, DDX24 knockdown with p53 stabilization readout\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro ubiquitylation reconstitution plus in vivo Co-IP, multiple functional readouts in single study\",\n      \"pmids\": [\"24980433\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"DDX24 interacts with p300, suppressing p300-mediated acetylation of p53; DDX24 overexpression inhibits the p300–p53 interaction, while DDX24 knockdown increases endogenous p53 acetylation, activates p21 and PUMA expression, and induces cell cycle arrest and senescence in a p53-dependent manner.\",\n      \"method\": \"Co-immunoprecipitation (DDX24–p300, p300–p53), acetylation assays, siRNA knockdown, cell cycle and senescence assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP plus acetylation assay plus p53-dependent rescue, multiple orthogonal methods\",\n      \"pmids\": [\"25867071\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"DDX24 mutations (including K11E and E271K in the ATP-binding domain) are associated with vascular malformations; DDX24 knockdown in endothelial cells elevates migration and tube formation, establishing a functional role in endothelial cell behavior.\",\n      \"method\": \"Genetic mutation analysis, structural modeling, siRNA knockdown, endothelial cell migration and tube formation assays, transcriptomic analysis\",\n      \"journal\": \"Hepatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — knockdown with defined cellular phenotype, genetic link; structural modeling is computational\",\n      \"pmids\": [\"30063812\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"LINC02551 acts as a molecular adaptor that blocks the interaction between DDX24 and the E3 ubiquitin ligase TRIM27, thereby decreasing ubiquitination and proteasomal degradation of DDX24 and promoting HCC progression; ALKBH5-mediated m6A demethylation of LINC02551 destabilizes LINC02551 and consequently reduces DDX24 protein.\",\n      \"method\": \"Co-immunoprecipitation (DDX24–TRIM27), ubiquitination assay, m6A modification analysis, knockdown/overexpression functional assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus ubiquitination assay plus functional rescue, single lab\",\n      \"pmids\": [\"36335087\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DDX24 binds the LAMB1 mRNA (nt 618–624) and increases its stability in a manner dependent on interaction between nucleolin and the C-terminal region of DDX24, promoting HCC migration and proliferation.\",\n      \"method\": \"RNA immunoprecipitation, mRNA stability assay, Co-immunoprecipitation (DDX24–nucleolin), overexpression/knockdown with migration/proliferation readouts\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RIP plus mRNA stability plus protein interaction, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"35763670\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DDX24 and DDX49 bind predominantly to immediate-early and early KSHV mRNAs (shown by RNA immunoprecipitation followed by next-generation sequencing) and exert antiviral activity by suppressing lytic viral transcription and genome replication when overexpressed in BCBL-1 cells.\",\n      \"method\": \"RNA immunoprecipitation-seq (tagged DDX24), overexpression in BCBL-1 cells, viral gene expression and replication assays, RNA pulldown with candidate transcripts\",\n      \"journal\": \"Viruses\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RIP-seq plus functional antiviral assay, single lab\",\n      \"pmids\": [\"36298642\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DDX24 interacts with RPL5 and promotes its ubiquitination and destabilization in NSCLC cells, enhancing cancer cell migration and invasion.\",\n      \"method\": \"Co-immunoprecipitation followed by mass spectrometry, protein stability assay, ubiquitination assay, knockdown/overexpression migration and invasion assays\",\n      \"journal\": \"Cancer medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP/MS plus ubiquitination assay, single lab\",\n      \"pmids\": [\"35864588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Loss-of-function mutations K11E and E271K in DDX24 reduce nucleolar number and cell proliferation, consistent with DDX24's role as an oncogenic factor in the nucleolus; these mutations decrease tumor formation in mouse xenograft models and alter immune-related signaling pathways.\",\n      \"method\": \"Stable cell line expression of WT and mutant DDX24, immunofluorescence (nucleoli counting), proliferation/colony assays, xenograft mouse models, transcriptome sequencing\",\n      \"journal\": \"International journal of medical sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple functional assays with defined mutations in vivo and in vitro\",\n      \"pmids\": [\"35370459\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DDX24 mutation E271K causes DDX24 to partition less into nucleoli; DDX24 directly associates with NPM1 and regulates its liquid-liquid phase separation behavior as a client in the nucleolar granular component; mutation or knockdown of DDX24 disrupts nucleolar homeostasis, impairs ribosome biogenesis, and elevates endothelial cell migration and tube formation.\",\n      \"method\": \"In vitro biomolecular condensate assay, Co-immunoprecipitation (DDX24–NPM1), immunofluorescence in patient tissues and ECs, knockdown and mutation functional assays (migration, tube formation, ribosome biogenesis)\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro phase separation plus Co-IP plus patient tissue validation, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"37705750\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DDX24 binds FANCA mRNA and stabilizes it; DDX24 loss leads to decreased FANCA, increased DNA damage, and cell cycle arrest in vascular smooth muscle cells; overexpression of FANCA rescues the DDX24-deficiency phenotype; VSMC-specific Ddx24 knockout mice die before E13.5 with defective vessel formation.\",\n      \"method\": \"RNA immunoprecipitation with qRT-PCR, RNA stability assay (RNA pulldown), VSMC-specific Cre-loxP knockout mice, flow cytometry, cell proliferation assay, rescue with FANCA overexpression\",\n      \"journal\": \"Arteriosclerosis, thrombosis, and vascular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — RIP, RNA pulldown, in vivo genetic knockout with epistatic rescue, multiple orthogonal methods\",\n      \"pmids\": [\"37470182\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DDX24 binds HK1 mRNA and positively regulates HK1 expression at the transcriptional level, promoting glycolysis (glucose uptake, lactate production) and tumor cell proliferation, migration, and invasion in gastric cancer.\",\n      \"method\": \"RNA binding assay (DDX24–HK1 mRNA), knockdown/overexpression with glycolysis readouts (glucose uptake, lactate), proliferation and migration assays\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, mRNA binding assay with functional follow-up, limited mechanistic detail\",\n      \"pmids\": [\"38043669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Endothelium-targeted Ddx24 conditional knockout (Cdh5-Cre system) in mice leads to elevated endothelial migration and tube formation, vascular hyper-permeability, and exacerbated ConA-induced hepatitis with elevated TNF-α and IFN-γ; mass spectrometry identified downregulation of vascular integrity-associated proteins.\",\n      \"method\": \"CRISPR/Cas9-mediated Cre-loxP conditional knockout, endothelial cell migration and tube formation assays, in vivo ConA hepatitis model, mass spectrometry of liver tissue proteins\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — conditional knockout with defined in vivo phenotype and MS-based protein profiling\",\n      \"pmids\": [\"38354508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DDX24 regulates alternative splicing of IKBKG pre-mRNA; DDX24 directly binds IKBKG pre-mRNA, and DDX24 ablation stimulates generation of the long IKBKG isoform, which activates NF-κB signaling, induces BECN1 transcription, and promotes autophagy to suppress lung cancer growth.\",\n      \"method\": \"Mass spectrometry (splicing interactome), RNA sequencing (alternative splicing), Co-immunoprecipitation, luciferase reporter assays, direct mRNA binding, xenograft tumor models, functional rescue with long IKBKG isoform\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (MS, RNAseq, Co-IP, reporter, rescue), single lab\",\n      \"pmids\": [\"39897555\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DDX24 deficiency in zebrafish endothelium enhances VEGFR2 expression by direct binding to its mRNA in non-brain endothelial cells, causing intersegmental vessel hyperbranching; in brain endothelial cells, DDX24 deficiency suppresses GPR124/RECK-mediated Wnt signaling; pharmacological rescue of both pathways in temporal sequence corrects the vascular phenotypes.\",\n      \"method\": \"Zebrafish ddx24 morpholino/mutant, direct mRNA binding assay (VEGFR2 mRNA), spatial transcriptome analysis, pharmacological epistasis, endothelial cell-type-specific dissection\",\n      \"journal\": \"PNAS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct mRNA binding plus in vivo genetic model plus pharmacological epistasis rescue, multiple orthogonal methods\",\n      \"pmids\": [\"40339127\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DDX24 binds PPFIA4 mRNA and enhances its stability; DDX24 knockdown reduces PPFIA4, causing occludin phosphorylation and mitochondrial dysfunction in cerebral microvascular endothelial cells; endothelial-specific Ddx24 KO mice show increased BBB permeability and learning/memory deficits; NADPH oxidase inhibition rescues these phenotypes.\",\n      \"method\": \"Endothelial-specific Ddx24 conditional knockout mice, RNA binding/stability assay (DDX24–PPFIA4 mRNA), Co-IP, occludin phosphorylation assay, mitochondrial function assay, NADPH oxidase inhibitor rescue, behavioral tests\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — conditional KO with defined in vivo phenotype, mRNA binding/stability, pharmacological rescue, multiple orthogonal methods\",\n      \"pmids\": [\"41105514\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DDX24 regulates HO-1 gene transcription (not mRNA stability) under oxidative stress, likely acting at the HO-1 promoter and enhancer E1 region; DDX24 depletion reduces HO-1 expression, cell viability, and anti-apoptotic/anti-oxidative capacity.\",\n      \"method\": \"RNA sequencing (DDX24-depleted vs. overexpressing cells), HO-1 promoter/enhancer reporter assays, mRNA stability assay, knockdown/overexpression with apoptosis and oxidative stress readouts\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reporter assay distinguishes transcriptional vs. post-transcriptional mechanism, plus mRNA stability assay, single lab\",\n      \"pmids\": [\"40847746\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"DDX24 directly binds specific endothelial mRNAs (including CLEC14A and ERG) identified by iCLIP-seq, and promotes their decay through interaction with the CCR4-NOT deadenylase complex, thereby regulating angiogenesis.\",\n      \"method\": \"Infrared cross-linking immunoprecipitation sequencing (iCLIP-seq), Co-immunoprecipitation (DDX24–CCR4-NOT complex), mRNA decay assays, endothelial functional assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — iCLIP-seq for direct binding plus Co-IP of CCR4-NOT complex plus mRNA decay assay, multiple orthogonal methods\",\n      \"pmids\": [\"41728947\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DDX24 is a nucleolar DEAD-box RNA helicase that directly binds specific mRNAs to regulate their stability or splicing (e.g., LAMB1, FANCA, VEGFR2, PPFIA4, IKBKG), promotes CCR4-NOT-dependent mRNA decay in endothelial cells, undergoes MDM2-mediated nonproteolytic polyubiquitylation to facilitate pre-rRNA processing, interacts with p300 to suppress p53 acetylation and with FADD/RIP1 to attenuate IRF7-driven type I interferon responses, is subject to TRIM27-mediated ubiquitination and proteasomal degradation (counteracted by the lncRNA LINC02551), and plays essential roles in vascular development, ribosome biogenesis, innate immune regulation, and cancer cell proliferation and migration.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"DDX24 is a DEAD-box RNA helicase that functions as a multifaceted post-transcriptional and transcriptional regulator essential for ribosome biogenesis, vascular development, and innate immune homeostasis. DDX24 directly binds specific mRNAs—including LAMB1, FANCA, VEGFR2, PPFIA4, and IKBKG—to regulate their stability or alternative splicing, and promotes CCR4-NOT-dependent mRNA decay of endothelial transcripts such as CLEC14A and ERG to control angiogenesis [PMID:41728947, PMID:37470182, PMID:40339127, PMID:39897555]. In the nucleolus, MDM2-mediated nonproteolytic polyubiquitylation of DDX24 facilitates its association with pre-rRNP complexes required for pre-rRNA processing, and DDX24 regulates nucleolar organization through NPM1-dependent liquid–liquid phase separation [PMID:24980433, PMID:37705750]. DDX24 additionally suppresses p53 activation by inhibiting p300-mediated p53 acetylation, attenuates RLR-mediated type I interferon responses by associating with FADD and RIP1, and is itself subject to TRIM27-mediated proteasomal degradation counteracted by the lncRNA LINC02551 [PMID:25867071, PMID:24204270, PMID:36335087].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Identification of DDX24 as a conserved DEAD-box family member established it as a candidate RNA helicase, but its cellular function remained unknown.\",\n      \"evidence\": \"cDNA cloning, Northern blot, and radiation hybrid mapping in human tissues\",\n      \"pmids\": [\"10936056\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No enzymatic or functional assay performed\", \"Helicase activity not demonstrated\", \"No subcellular localization determined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Linking DDX24 to HIV-1 Rev-dependent RNA packaging provided the first functional evidence that DDX24 participates in nuclear RNA export and viral RNA metabolism.\",\n      \"evidence\": \"siRNA knockdown, HIV-1 RNA packaging assay, and Co-IP of DDX24–Rev interaction\",\n      \"pmids\": [\"18289627\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether DDX24 directly unwinds viral RNA structures not tested\", \"Role in endogenous mRNA export not addressed\", \"Single viral system\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Discovery that DDX24 suppresses RLR-mediated type I interferon signaling through FADD/RIP1 interaction established it as a negative regulator of innate immunity, revealing a non-canonical function beyond RNA metabolism.\",\n      \"evidence\": \"Overexpression/knockdown reporter assays, Co-IP of DDX24–FADD and DDX24–RIP1, RNA vs. DNA binding assays\",\n      \"pmids\": [\"24204270\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise mechanism of IRF7 inhibition not defined at the structural level\", \"Whether helicase activity is required for immune suppression not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrating that MDM2 mediates nonproteolytic polyubiquitylation of DDX24 to promote its association with pre-rRNP complexes resolved how DDX24 enters the ribosome biogenesis pathway and connected ribosomal stress to p53 stabilization.\",\n      \"evidence\": \"In vitro and in vivo ubiquitylation assays, Co-IP of DDX24–MDM2, pre-rRNA processing assays, p53 stabilization readout\",\n      \"pmids\": [\"24980433\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which specific pre-rRNA processing step DDX24 catalyzes remains unclear\", \"Ubiquitylation sites on DDX24 not mapped\", \"Direct helicase activity on pre-rRNA not shown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Finding that DDX24 inhibits p300-mediated p53 acetylation explained how DDX24 depletion activates p53 target genes (p21, PUMA), linking DDX24 to cell cycle control and senescence independently of ribosomal stress.\",\n      \"evidence\": \"Co-IP of DDX24–p300 and p300–p53, acetylation assays, siRNA knockdown with cell cycle and senescence readouts\",\n      \"pmids\": [\"25867071\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the DDX24–p300 interaction requires RNA binding or helicase activity is unknown\", \"Relationship between nucleolar and p300-mediated p53 regulation not dissected\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identification of DDX24 mutations (K11E, E271K) in patients with vascular malformations provided the first genetic evidence that DDX24 loss-of-function causes human vascular disease, linking its molecular functions to endothelial biology.\",\n      \"evidence\": \"Genetic mutation analysis, siRNA knockdown in endothelial cells with migration and tube formation assays\",\n      \"pmids\": [\"30063812\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal mechanism by which mutations cause vascular malformations not fully defined\", \"Patient cohort limited\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Multiple studies in 2022 established DDX24 as a direct mRNA-binding protein that stabilizes LAMB1 mRNA (via nucleolin interaction), promotes RPL5 ubiquitination and degradation, and suppresses KSHV lytic replication, broadening its role to post-transcriptional regulation and cancer cell proliferation.\",\n      \"evidence\": \"RNA immunoprecipitation, mRNA stability assays, Co-IP/MS (DDX24–RPL5, DDX24–nucleolin), RIP-seq in KSHV-infected cells, knockdown/overexpression with functional readouts\",\n      \"pmids\": [\"35763670\", \"35864588\", \"36298642\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether mRNA stabilization requires helicase activity is untested\", \"RPL5 ubiquitination mechanism (direct vs. adaptor) unclear\", \"KSHV antiviral mechanism is descriptive\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstration that TRIM27 ubiquitylates DDX24 for proteasomal degradation and that LINC02551 blocks this interaction revealed a regulatory axis controlling DDX24 protein levels in hepatocellular carcinoma, connecting m6A RNA modification to DDX24 abundance.\",\n      \"evidence\": \"Co-IP of DDX24–TRIM27, ubiquitination assays, m6A modification analysis, functional rescue\",\n      \"pmids\": [\"36335087\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"TRIM27 ubiquitination sites on DDX24 not mapped\", \"Single cancer type studied\", \"LINC02551 structural basis for blocking TRIM27 unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showing that DDX24 associates with NPM1 and modulates nucleolar liquid–liquid phase separation explained how DDX24 mutations disrupt nucleolar organization and ribosome biogenesis, connecting phase behavior to the vascular phenotype.\",\n      \"evidence\": \"In vitro biomolecular condensate assay, Co-IP of DDX24–NPM1, immunofluorescence in patient tissues, knockdown/mutation functional assays\",\n      \"pmids\": [\"37705750\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether DDX24 helicase activity drives phase separation partitioning not tested\", \"Contribution of phase separation vs. enzymatic activity to ribosome biogenesis not separated\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Conditional VSMC-specific Ddx24 knockout causing embryonic lethality before E13.5 with defective vessel formation, rescued by FANCA overexpression, established DDX24-dependent FANCA mRNA stabilization as essential for vascular smooth muscle cell survival and vessel integrity.\",\n      \"evidence\": \"VSMC-specific Cre-loxP knockout mice, RNA immunoprecipitation, mRNA stability assay, FANCA rescue\",\n      \"pmids\": [\"37470182\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"DDX24 binding site on FANCA mRNA not mapped at nucleotide resolution\", \"Whether other mRNA targets contribute to the VSMC lethal phenotype not excluded\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Several 2025 studies revealed DDX24 as a versatile mRNA regulator in the vasculature: it directly binds VEGFR2 mRNA to limit angiogenic sprouting in zebrafish, stabilizes PPFIA4 mRNA to maintain blood-brain barrier integrity, and regulates IKBKG pre-mRNA splicing to control NF-κB-driven autophagy in lung cancer.\",\n      \"evidence\": \"Zebrafish morpholino/mutant with pharmacological epistasis, endothelial-specific Ddx24 KO mice with BBB permeability and behavioral tests, RNA-seq-based alternative splicing analysis with functional rescue in xenografts\",\n      \"pmids\": [\"40339127\", \"41105514\", \"39897555\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for DDX24 target mRNA selectivity not resolved\", \"Whether splicing regulation is direct unwinding or scaffolding is unclear\", \"Brain vs. non-brain endothelial target specificity mechanism unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of DDX24 as a transcriptional regulator of HO-1 under oxidative stress, acting at the promoter/enhancer rather than on mRNA stability, expanded its functional repertoire beyond post-transcriptional regulation.\",\n      \"evidence\": \"HO-1 promoter/enhancer reporter assays, mRNA stability assay ruling out post-transcriptional effect, knockdown/overexpression with oxidative stress readouts\",\n      \"pmids\": [\"40847746\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether DDX24 binds chromatin directly or acts through a transcription factor complex unknown\", \"Mechanism distinguishing transcriptional from post-transcriptional target selection unclear\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Transcriptome-wide iCLIP-seq mapping of DDX24 binding sites coupled with demonstration of CCR4-NOT complex interaction established that DDX24 recruits the deadenylase machinery to specific endothelial mRNAs to promote their decay, providing a unifying mechanism for its mRNA-destabilizing activities.\",\n      \"evidence\": \"iCLIP-seq for direct binding, Co-IP of DDX24–CCR4-NOT complex, mRNA decay assays in endothelial cells\",\n      \"pmids\": [\"41728947\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether DDX24 helicase activity is required for CCR4-NOT recruitment not tested\", \"How DDX24 distinguishes mRNAs it stabilizes from those it promotes for decay is unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A central unresolved question is how DDX24 selects between stabilizing and destabilizing mRNA targets, and whether its enzymatic helicase activity—as opposed to scaffolding—is required for each of its diverse functions in ribosome biogenesis, mRNA regulation, innate immunity, and transcription.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No crystal or cryo-EM structure of DDX24 alone or in complex\", \"Helicase activity has never been directly measured in vitro on any substrate\", \"Selectivity rules for mRNA stabilization vs. CCR4-NOT-dependent decay are unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [2, 7, 8, 12, 15, 16, 17, 19]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [7, 12, 15, 17, 19]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 4, 15]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [18]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [3, 10, 11]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 3, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [7, 12, 15, 16, 17, 19]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [3, 9, 11]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [2, 14]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [18]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [5, 12, 16]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [15]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3, 11]}\n    ],\n    \"complexes\": [\n      \"CCR4-NOT deadenylase complex\"\n    ],\n    \"partners\": [\n      \"MDM2\",\n      \"NPM1\",\n      \"TRIM27\",\n      \"FADD\",\n      \"RIP1\",\n      \"TP53\",\n      \"EP300\",\n      \"NCL\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}