{"gene":"DDX56","run_date":"2026-06-09T23:54:41","timeline":{"discoveries":[{"year":2000,"finding":"NOH61/DDX56 is a nucleolar DEAD-box protein with demonstrated ATPase activity that is stimulated by polynucleotides; it sediments as homo-oligomeric structures in vitro (~11.5S) but as a monomer (~4S) under high-salt conditions; it is a constituent of free nucleoplasmic 65S preribosomal particles but absent from cytoplasmic ribosomes; its nucleolar localization is disrupted by actinomycin D or RNase A treatment, indicating RNA-dependent nucleolar association.","method":"ATPase activity assay with recombinant protein, sucrose gradient sedimentation, immunolocalization, RNase A and actinomycin D treatment of cultured cells, biochemical fractionation","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal biochemical methods (ATPase assay, sedimentation, fractionation, localization) in a single focused study","pmids":["10749921"],"is_preprint":false},{"year":2011,"finding":"DDX56 interacts with West Nile virus (WNV) capsid protein in infected cells (interaction confirmed by co-immunoprecipitation and shown to be RNA-independent); WNV infection induces relocalization of DDX56 from the nucleolus to a cytoplasmic compartment containing capsid protein; DDX56 is not required for WNV RNA replication but is required for assembly of infectious virions—virions from DDX56-depleted cells contain less viral RNA and are ~100-fold less infectious.","method":"Yeast two-hybrid screen, co-immunoprecipitation (RNA-independent), siRNA knockdown, viral infectivity assays, immunofluorescence/localization studies","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, siRNA knockdown with specific infectivity phenotype, multiple orthogonal methods in a single rigorous study","pmids":["21411523"],"is_preprint":false},{"year":2012,"finding":"The helicase enzymatic activity of DDX56 is essential for its role in WNV virion assembly; overexpression of the capsid-binding region of DDX56 (acting as a dominant negative) reduces WNV infectivity, indicating that the DDX56–capsid interaction is a functionally important step in the virion assembly pathway.","method":"Helicase-dead mutant overexpression, dominant-negative capsid-binding domain overexpression, viral infectivity assays","journal":"Virology","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — enzymatic mutant combined with dominant-negative approach and infectivity readout, single lab with two orthogonal approaches","pmids":["22925334"],"is_preprint":false},{"year":2016,"finding":"During WNV infection DDX56 relocalizes from nucleoli to virus assembly sites on the endoplasmic reticulum (ER); super-resolution microscopy shows capsid and DDX56 occupy the same ER subcompartment; however, stable interaction between DDX56 and capsid is only detected in the nucleus, suggesting the cytoplasmic interaction is transient during virion morphogenesis.","method":"Super-resolution microscopy, co-immunoprecipitation from nuclear and cytoplasmic fractions, immunofluorescence colocalization","journal":"Virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — super-resolution imaging + fractionation Co-IP, single lab, two orthogonal methods","pmids":["27821284"],"is_preprint":false},{"year":2019,"finding":"DDX56 interacts with FMDV non-structural protein 3A and cooperates with it to inhibit type I interferon signaling by reducing IRF3 phosphorylation, thereby promoting FMDV replication; the D166 residue of DDX56 is required for both promoting replication and inhibiting IRF3 phosphorylation in cooperation with 3A.","method":"Co-immunoprecipitation, siRNA knockdown, overexpression, IRF3 phosphorylation assay, viral replication assays, site-directed mutagenesis (D166)","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, mutagenesis, and functional knockdown/overexpression in single lab study","pmids":["31445188"],"is_preprint":false},{"year":2020,"finding":"During chikungunya virus (CHIKV) infection, DDX56 relocalizes from the nucleus to the cytoplasm; in the cytoplasm it binds a predicted stem-loop structure on the incoming viral genomic RNA (identified by CLIP-Seq) and destabilizes it, attenuating infection at the earliest step of the replication cycle through an interferon-independent mechanism; this antiviral function is conserved between Drosophila and human cells.","method":"RNA interference screen, CLIP-Seq, viral infection assays with DDX56 depletion, immunofluorescence localization, Drosophila genetic knockdown","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Strong — CLIP-Seq identifies specific RNA binding site, genetic knockdown with phenotypic readout replicated in two organisms (Drosophila and human cells), multiple orthogonal methods","pmids":["33109765"],"is_preprint":false},{"year":2021,"finding":"DDX56 interacts with the IAV NS1 protein (confirmed by yeast two-hybrid and co-immunoprecipitation in mammalian cells); DDX56 knockdown significantly reduces influenza A virus replication, indicating DDX56 is a positive host factor for IAV replication.","method":"Yeast two-hybrid, co-immunoprecipitation in mammalian cells, colocalization by immunofluorescence, siRNA knockdown with viral replication assay","journal":"Genetics and molecular biology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP confirmed in mammalian cells, knockdown phenotype, single lab with two orthogonal binding assays","pmids":["33749700"],"is_preprint":false},{"year":2021,"finding":"DDX56 promotes EMCV replication by inhibiting IRF3 phosphorylation and nuclear translocation; mechanistically, DDX56 directly targets importin subunits KPNA3 and KPNA4 to block IRF3 nuclear import in the MDA5-triggered signaling cascade, thereby suppressing IFN-β production.","method":"Overexpression/knockdown viral replication assays, IRF3 phosphorylation and nuclear translocation assays, co-immunoprecipitation with KPNA3/KPNA4, IFN-β reporter assays","journal":"Veterinary microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with specific importin targets, nuclear translocation assays, knockdown phenotype, single lab with multiple methods","pmids":["34922148"],"is_preprint":false},{"year":2020,"finding":"Ddx56 is required for ribosome assembly in mouse embryonic stem cells (mESCs); knockout or knockdown of Ddx56 causes ribosome dysfunction and cell lethality; separately, Ddx56 interacts with the Oct4/Sox2 pluripotency complex by binding to Sox2 (confirmed by co-IP), and a C-terminal truncation (Ddx56 ΔC-ter) that does not affect ribosome assembly shows reduced Sox2 interaction and decreased mESC proliferation.","method":"Knockout/RNAi knockdown, polysome fractionation, co-immunoprecipitation, RNA sequencing, C-terminal truncation mutant analysis","journal":"Stem cell research & therapy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — polysome fractionation + Co-IP + domain-deletion mutant, single lab with multiple orthogonal methods","pmids":["32703285"],"is_preprint":false},{"year":2021,"finding":"DDX56 promotes SqCLC cell growth and migration by post-transcriptionally upregulating Wnt pathway genes (CTNNB1, WNT2B); mechanistically, DDX56 facilitates degradation of primary miR-378a, leading to reduced mature miR-378a-3p and consequent derepression of WNT2B.","method":"siRNA knockdown and overexpression in vitro, xenograft in vivo, miRNA profiling, qRT-PCR for pri-miR-378a processing","journal":"Molecular cancer","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — functional knockdown/overexpression with specific miRNA processing readout, in vitro and in vivo, single lab","pmids":["34446021"],"is_preprint":false},{"year":2021,"finding":"In glioblastoma stem cells, DDX56 localizes to the nucleolus; loss of DDX56 in planarians causes dysregulation of ribosomal RNA expression and loss of nucleolar integrity prior to stem cell death, indicating a conserved role for DDX56 in nucleolar/ribosomal RNA biology in stem cells.","method":"Comparative genomics, RNAi knockdown in planarians, nucleolar integrity assays (microscopy), human GSC functional assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cross-species genetic knockdown with specific rRNA and nucleolar phenotype, replicated in multiple stem cell systems","pmids":["33789112"],"is_preprint":false},{"year":2022,"finding":"DDX56 interacts with MECOM to promote mono-methylation of H3K9 (H3K9me1) on the MIST1 promoter, leading to enhanced MIST1 transcription and subsequent activation of PTEN/AKT signaling in HCC; ZEB1 transcriptionally activates DDX56 expression; DDX56 occupancy on the MIST1 promoter was confirmed by ChIP and EMSA.","method":"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), dual-luciferase reporter, in vitro/in vivo xenograft models, siRNA knockdown and overexpression","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP + EMSA + luciferase reporter with Co-IP, single lab with multiple orthogonal methods","pmids":["36168636"],"is_preprint":false},{"year":2022,"finding":"DDX56 directly interacts with cGAS and promotes cGAS expression; this interaction enhances cGAS-STING-IFN-β signaling, including promoting IRF3 phosphorylation and nuclear translocation, thereby inhibiting pseudorabies virus (PRV) replication; knockdown of cGAS abrogates the antiviral and IFN-β-promoting effects of DDX56.","method":"Co-immunoprecipitation, overexpression/knockdown, IRF3 phosphorylation/translocation assays, cGAS knockdown epistasis, IFN-β reporter/quantification","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with epistasis (cGAS knockdown reversal), multiple functional readouts, single lab","pmids":["36090064"],"is_preprint":false},{"year":2024,"finding":"DDX56 promotes HCC EMT and cancer stemness through the MELK-FOXM1 signaling axis; DDX56 enhances MELK-mediated FOXM1 expression, regulating cancer stemness and malignant traits; knockdown of DDX56 in vivo reduced tumorigenicity and lung metastasis.","method":"siRNA knockdown and overexpression in vitro, in vivo tumor-bearing mouse model, EMT and stemness marker assays, MELK-FOXM1 pathway analysis","journal":"iScience","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, pathway-level phenotypic analysis without direct binding or biochemical demonstration of DDX56–MELK interaction mechanism","pmids":["38827395"],"is_preprint":false}],"current_model":"DDX56 (NOH61) is a nucleolar DEAD-box RNA helicase with intrinsic ATPase activity that participates in 60S ribosomal subunit biogenesis (residing in 65S preribosomal particles), interacts with the Oct4/Sox2 pluripotency complex via Sox2 to support stem cell proliferation, and is co-opted by multiple RNA viruses: its helicase activity and interaction with WNV capsid protein are required for assembly of infectious WNV virions at ER assembly sites; it binds a stem-loop in the CHIKV genome to destabilize incoming viral RNA in an interferon-independent antiviral mechanism; and it suppresses type I interferon responses for FMDV and EMCV by inhibiting IRF3 phosphorylation/nuclear translocation through distinct mechanisms (interaction with FMDV 3A or targeting of importins KPNA3/KPNA4), while for PRV it enhances IFN-β through direct interaction with cGAS; in cancer contexts DDX56 promotes oncogenesis via H3K9 methylation-mediated transcriptional activation of MIST1/PTEN-AKT and miRNA-mediated post-transcriptional regulation of Wnt signaling."},"narrative":{"mechanistic_narrative":"DDX56 (NOH61) is a nucleolar DEAD-box RNA helicase with polynucleotide-stimulated ATPase activity that functions in 60S ribosomal subunit biogenesis, residing in free nucleoplasmic 65S preribosomal particles and showing RNA-dependent nucleolar localization that is lost upon actinomycin D or RNase A treatment [PMID:10749921]. This ribosome-assembly role is conserved across stem cell systems: Ddx56 is required for ribosome assembly and viability in mouse embryonic stem cells, where it also binds the Oct4/Sox2 pluripotency complex through Sox2 via its C-terminus to support proliferation independently of its ribosome function [PMID:32703285], and its loss in planarians and human glioblastoma stem cells dysregulates rRNA and disrupts nucleolar integrity prior to stem cell death [PMID:33789112]. DDX56 is repeatedly co-opted at the host–virus interface. For West Nile virus it relocalizes from the nucleolus to ER assembly sites, binds the capsid protein in an RNA-independent manner, and uses its helicase activity to support assembly of infectious virions without affecting RNA replication [PMID:21411523, PMID:22925334, PMID:27821284]. In innate immunity DDX56 acts as both a proviral suppressor and an antiviral effector depending on context: it inhibits type I interferon signaling for FMDV by cooperating with the 3A protein to block IRF3 phosphorylation (requiring residue D166) [PMID:31445188] and for EMCV by targeting importins KPNA3/KPNA4 to prevent IRF3 nuclear import [PMID:34922148], yet it directly binds a stem-loop in incoming chikungunya virus genomic RNA to destabilize it in an interferon-independent manner [PMID:33109765] and enhances cGAS-STING-IFN-β signaling against pseudorabies virus through direct interaction with cGAS [PMID:36090064]. In cancer, DDX56 drives oncogenic transcriptional and post-transcriptional programs, partnering with MECOM to deposit H3K9me1 at the MIST1 promoter and activate PTEN-AKT signaling in HCC [PMID:36168636] and promoting Wnt signaling by facilitating degradation of pri-miR-378a [PMID:34446021].","teleology":[{"year":2000,"claim":"Established the basic biochemical identity of DDX56 as a nucleolar DEAD-box ATPase and placed it in the ribosome biogenesis pathway, answering what kind of enzyme it is and where it acts.","evidence":"Recombinant ATPase assay, sucrose gradient sedimentation, biochemical fractionation and immunolocalization with actinomycin D/RNase A treatment in cultured cells","pmids":["10749921"],"confidence":"High","gaps":["RNA substrate specificity of helicase activity not defined","specific step in 60S maturation not pinpointed","no structural model of oligomerization"]},{"year":2011,"claim":"Showed DDX56 is hijacked by West Nile virus as a host assembly factor, distinguishing its role from RNA replication and linking it to capsid via direct binding.","evidence":"Yeast two-hybrid, RNA-independent co-immunoprecipitation, siRNA knockdown and viral infectivity assays in infected cells","pmids":["21411523"],"confidence":"High","gaps":["molecular mechanism by which DDX56 packages viral RNA unresolved","did not address helicase requirement"]},{"year":2012,"claim":"Demonstrated that the helicase enzymatic activity and the capsid-binding interaction are functionally required for WNV virion assembly, moving from correlation to mechanism.","evidence":"Helicase-dead mutant and dominant-negative capsid-binding domain overexpression with infectivity readouts","pmids":["22925334"],"confidence":"High","gaps":["RNA substrate acted upon during assembly unknown","stoichiometry of capsid complex undefined"]},{"year":2016,"claim":"Refined the spatial model of WNV co-option, showing DDX56 and capsid colocalize at ER assembly sites while stable binding occurs in the nucleus, implying a transient cytoplasmic interaction.","evidence":"Super-resolution microscopy and fractionated co-immunoprecipitation","pmids":["27821284"],"confidence":"Medium","gaps":["transient cytoplasmic interaction not directly captured biochemically","trigger for nucleolar-to-ER relocalization unknown"]},{"year":2020,"claim":"Separated DDX56's ribosome-assembly role from a distinct pluripotency function in stem cells, using a domain mutant to dissociate the two activities.","evidence":"Knockout/RNAi, polysome fractionation, co-IP with Sox2 and C-terminal truncation mutant analysis in mESCs","pmids":["32703285"],"confidence":"Medium","gaps":["mechanism of Sox2-DDX56 cooperation in proliferation undefined","whether helicase activity contributes to pluripotency role unaddressed"]},{"year":2020,"claim":"Revealed an intrinsic antiviral activity in which DDX56 directly recognizes and destabilizes viral genomic RNA, contrasting with its proviral roles.","evidence":"RNAi screen, CLIP-Seq mapping of a stem-loop binding site, infection assays in human and Drosophila cells","pmids":["33109765"],"confidence":"High","gaps":["mechanism of RNA destabilization (helicase vs recruitment of nucleases) not resolved","how DDX56 distinguishes viral from host RNA unknown"]},{"year":2021,"claim":"Extended DDX56's interferon-suppressive proviral function to EMCV through a specific block on IRF3 nuclear import via importin targeting.","evidence":"Co-IP with KPNA3/KPNA4, IRF3 phosphorylation/translocation assays, IFN-β reporter and knockdown in the MDA5 cascade","pmids":["34922148"],"confidence":"Medium","gaps":["direct vs indirect KPNA binding not structurally defined","relationship to FMDV mechanism not reconciled"]},{"year":2021,"claim":"Identified DDX56 as a positive host factor for influenza A virus via interaction with NS1, broadening the range of viruses that exploit it.","evidence":"Yeast two-hybrid, mammalian co-IP, colocalization and siRNA knockdown with replication assay","pmids":["33749700"],"confidence":"Medium","gaps":["functional consequence of NS1 binding mechanistically undefined","single-lab interaction without reciprocal mapping"]},{"year":2021,"claim":"Connected DDX56 to oncogenic Wnt signaling through a post-transcriptional miRNA-processing mechanism, expanding its functional repertoire beyond viral and ribosomal roles.","evidence":"Knockdown/overexpression in vitro, xenograft, miRNA profiling and pri-miR-378a processing qRT-PCR in squamous cell lung carcinoma","pmids":["34446021"],"confidence":"Medium","gaps":["direct binding of DDX56 to pri-miR-378a not demonstrated","helicase requirement for miRNA degradation untested"]},{"year":2021,"claim":"Established conservation of DDX56's nucleolar/rRNA role in stem cell maintenance across species, tying ribosome biology to stem cell survival.","evidence":"Comparative genomics, planarian RNAi with nucleolar integrity and rRNA assays, human GSC functional assays","pmids":["33789112"],"confidence":"Medium","gaps":["direct rRNA processing step affected not defined","link between nucleolar disruption and cell death mechanistically unmapped"]},{"year":2022,"claim":"Defined a chromatin-level oncogenic mechanism in which DDX56 partners with MECOM to deposit H3K9me1 and activate the MIST1/PTEN-AKT axis in HCC.","evidence":"Co-IP, ChIP, EMSA, dual-luciferase reporter and xenograft models with knockdown/overexpression","pmids":["36168636"],"confidence":"Medium","gaps":["how an RNA helicase confers promoter occupancy/methyltransferase recruitment unclear","direct vs MECOM-dependent DNA binding not separated"]},{"year":2022,"claim":"Showed a context-specific antiviral role in which DDX56 directly binds cGAS to enhance IFN-β signaling against PRV, contrasting with its IFN-suppressive activity in other infections.","evidence":"Co-IP, cGAS-knockdown epistasis, IRF3 phosphorylation/translocation and IFN-β assays","pmids":["36090064"],"confidence":"Medium","gaps":["determinant of pro- vs anti-interferon switching across viruses unknown","structural basis of cGAS interaction undefined"]},{"year":2024,"claim":"Proposed an additional oncogenic axis linking DDX56 to EMT and stemness via MELK-FOXM1 signaling in HCC.","evidence":"Knockdown/overexpression in vitro, in vivo metastasis model and EMT/stemness marker analysis","pmids":["38827395"],"confidence":"Low","gaps":["no direct DDX56-MELK binding or biochemical mechanism demonstrated","pathway-level phenotype only","relationship to other oncogenic axes unclear"]},{"year":null,"claim":"What determines whether DDX56 acts as a proviral interferon suppressor or an antiviral effector, and how its core helicase/ATPase activity is mechanistically deployed across ribosome assembly, viral RNA destabilization, and chromatin/miRNA regulation, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["unifying biochemical mechanism linking diverse roles absent","no structural data for any partner interaction","RNA substrate determinants undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,5]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[0]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,2]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0,10]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,5]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[4,7,12]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[1,5,9,11]}],"complexes":[],"partners":["WNV CAPSID","SOX2","FMDV 3A","KPNA3","KPNA4","NS1","CGAS","MECOM"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NY93","full_name":"Probable ATP-dependent RNA helicase DDX56","aliases":["ATP-dependent 61 kDa nucleolar RNA helicase","DEAD box protein 21","DEAD box protein 56"],"length_aa":547,"mass_kda":61.6,"function":"Nucleolar RNA helicase that plays a role in various biological processes including innate immunity, ribosome biogenesis or nucleolus organization (PubMed:31340999, PubMed:33789112). Plays an essential role in maintaining nucleolar integrity in planarian stem cells (PubMed:33789112). Maintains embryonic stem cells proliferation by conventional regulation of ribosome assembly and interaction with OCT4 and POU5F1 complex (By similarity). Regulates antiviral innate immunity by inhibiting the virus-triggered signaling nuclear translocation of IRF3 (PubMed:31340999). Mechanistically, acts by disrupting the interaction between IRF3 and importin IPO5 (PubMed:31340999). May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity (Microbial infection) Helicase activity is important for packaging viral RNA into virions during West Nile virus infection (Microbial infection) Plays a positive role in foot-and-mouth disease virus replication by inhibiting the phosphorylation of IRF3 leading to inhibition of type I interferon (Microbial infection) Plays a positive role in EMCV replication by interrupting IRF3 phosphorylation and its nucleus translocation","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q9NY93/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/DDX56","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000136271","cell_line_id":"CID001064","localizations":[{"compartment":"nucleolus_gc","grade":3},{"compartment":"cytoplasmic","grade":1}],"interactors":[{"gene":"PPP2R5E","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001064","total_profiled":1310},"omim":[{"mim_id":"608023","title":"DEAD-BOX HELICASE 56; DDX56","url":"https://www.omim.org/entry/608023"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoli","reliability":"Supported"},{"location":"Mitotic chromosome","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DDX56"},"hgnc":{"alias_symbol":["NOH61"],"prev_symbol":[]},"alphafold":{"accession":"Q9NY93","domains":[{"cath_id":"3.40.50.300","chopping":"8-70_77-218","consensus_level":"high","plddt":87.59,"start":8,"end":218},{"cath_id":"3.40.50.300","chopping":"230-321_345-437_483-500","consensus_level":"high","plddt":83.72,"start":230,"end":500}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NY93","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NY93-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NY93-F1-predicted_aligned_error_v6.png","plddt_mean":79.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DDX56","jax_strain_url":"https://www.jax.org/strain/search?query=DDX56"},"sequence":{"accession":"Q9NY93","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NY93.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NY93/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NY93"}},"corpus_meta":[{"pmid":"21411523","id":"PMC_21411523","title":"The capsid-binding nucleolar helicase DDX56 is important for infectivity of West Nile virus.","date":"2011","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/21411523","citation_count":74,"is_preprint":false},{"pmid":"10749921","id":"PMC_10749921","title":"A novel helicase-type protein in the nucleolus: protein NOH61.","date":"2000","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/10749921","citation_count":58,"is_preprint":false},{"pmid":"22925334","id":"PMC_22925334","title":"The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles.","date":"2012","source":"Virology","url":"https://pubmed.ncbi.nlm.nih.gov/22925334","citation_count":49,"is_preprint":false},{"pmid":"27821284","id":"PMC_27821284","title":"The nucleolar helicase DDX56 redistributes to West Nile virus assembly sites.","date":"2016","source":"Virology","url":"https://pubmed.ncbi.nlm.nih.gov/27821284","citation_count":33,"is_preprint":false},{"pmid":"31445188","id":"PMC_31445188","title":"DDX56 cooperates with FMDV 3A to enhance FMDV replication by inhibiting the phosphorylation of IRF3.","date":"2019","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/31445188","citation_count":26,"is_preprint":false},{"pmid":"34446021","id":"PMC_34446021","title":"DDX56 modulates post-transcriptional Wnt signaling through miRNAs and is associated with early recurrence in squamous cell lung carcinoma.","date":"2021","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/34446021","citation_count":25,"is_preprint":false},{"pmid":"33109765","id":"PMC_33109765","title":"DDX56 Binds to Chikungunya Virus RNA To Control Infection.","date":"2020","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/33109765","citation_count":24,"is_preprint":false},{"pmid":"36168636","id":"PMC_36168636","title":"DDX56 transcriptionally activates MIST1 to facilitate tumorigenesis of HCC through PTEN-AKT signaling.","date":"2022","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/36168636","citation_count":23,"is_preprint":false},{"pmid":"33789112","id":"PMC_33789112","title":"The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/33789112","citation_count":17,"is_preprint":false},{"pmid":"38827395","id":"PMC_38827395","title":"DDX56 promotes EMT and cancer stemness via MELK-FOXM1 axis in hepatocellular carcinoma.","date":"2024","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/38827395","citation_count":13,"is_preprint":false},{"pmid":"33749700","id":"PMC_33749700","title":"Human DDX56 protein interacts with influenza A virus NS1 protein and stimulates the virus replication.","date":"2021","source":"Genetics and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/33749700","citation_count":12,"is_preprint":false},{"pmid":"34922148","id":"PMC_34922148","title":"DDX56 antagonizes IFN-β production to enhance EMCV replication by inhibiting IRF3 nuclear translocation.","date":"2021","source":"Veterinary microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/34922148","citation_count":11,"is_preprint":false},{"pmid":"32703285","id":"PMC_32703285","title":"Ddx56 maintains proliferation of mouse embryonic stem cells via ribosome assembly and interaction with the Oct4/Sox2 complex.","date":"2020","source":"Stem cell research & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/32703285","citation_count":11,"is_preprint":false},{"pmid":"36090064","id":"PMC_36090064","title":"DDX56 inhibits PRV replication through regulation of IFN-β signaling pathway by targeting cGAS.","date":"2022","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/36090064","citation_count":7,"is_preprint":false},{"pmid":"40670701","id":"PMC_40670701","title":"Identifying the crucial oncogenic mechanisms of DDX56 based on a machine learning-based integration model of RNA-binding proteins.","date":"2025","source":"NPJ precision oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40670701","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8707,"output_tokens":3800,"usd":0.041561,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11596,"output_tokens":4247,"usd":0.082077,"stage2_stop_reason":"end_turn"},"total_usd":0.123638,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"NOH61/DDX56 is a nucleolar DEAD-box protein with demonstrated ATPase activity that is stimulated by polynucleotides; it sediments as homo-oligomeric structures in vitro (~11.5S) but as a monomer (~4S) under high-salt conditions; it is a constituent of free nucleoplasmic 65S preribosomal particles but absent from cytoplasmic ribosomes; its nucleolar localization is disrupted by actinomycin D or RNase A treatment, indicating RNA-dependent nucleolar association.\",\n      \"method\": \"ATPase activity assay with recombinant protein, sucrose gradient sedimentation, immunolocalization, RNase A and actinomycin D treatment of cultured cells, biochemical fractionation\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal biochemical methods (ATPase assay, sedimentation, fractionation, localization) in a single focused study\",\n      \"pmids\": [\"10749921\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"DDX56 interacts with West Nile virus (WNV) capsid protein in infected cells (interaction confirmed by co-immunoprecipitation and shown to be RNA-independent); WNV infection induces relocalization of DDX56 from the nucleolus to a cytoplasmic compartment containing capsid protein; DDX56 is not required for WNV RNA replication but is required for assembly of infectious virions—virions from DDX56-depleted cells contain less viral RNA and are ~100-fold less infectious.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation (RNA-independent), siRNA knockdown, viral infectivity assays, immunofluorescence/localization studies\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, siRNA knockdown with specific infectivity phenotype, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"21411523\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The helicase enzymatic activity of DDX56 is essential for its role in WNV virion assembly; overexpression of the capsid-binding region of DDX56 (acting as a dominant negative) reduces WNV infectivity, indicating that the DDX56–capsid interaction is a functionally important step in the virion assembly pathway.\",\n      \"method\": \"Helicase-dead mutant overexpression, dominant-negative capsid-binding domain overexpression, viral infectivity assays\",\n      \"journal\": \"Virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — enzymatic mutant combined with dominant-negative approach and infectivity readout, single lab with two orthogonal approaches\",\n      \"pmids\": [\"22925334\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"During WNV infection DDX56 relocalizes from nucleoli to virus assembly sites on the endoplasmic reticulum (ER); super-resolution microscopy shows capsid and DDX56 occupy the same ER subcompartment; however, stable interaction between DDX56 and capsid is only detected in the nucleus, suggesting the cytoplasmic interaction is transient during virion morphogenesis.\",\n      \"method\": \"Super-resolution microscopy, co-immunoprecipitation from nuclear and cytoplasmic fractions, immunofluorescence colocalization\",\n      \"journal\": \"Virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — super-resolution imaging + fractionation Co-IP, single lab, two orthogonal methods\",\n      \"pmids\": [\"27821284\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"DDX56 interacts with FMDV non-structural protein 3A and cooperates with it to inhibit type I interferon signaling by reducing IRF3 phosphorylation, thereby promoting FMDV replication; the D166 residue of DDX56 is required for both promoting replication and inhibiting IRF3 phosphorylation in cooperation with 3A.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, overexpression, IRF3 phosphorylation assay, viral replication assays, site-directed mutagenesis (D166)\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, mutagenesis, and functional knockdown/overexpression in single lab study\",\n      \"pmids\": [\"31445188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"During chikungunya virus (CHIKV) infection, DDX56 relocalizes from the nucleus to the cytoplasm; in the cytoplasm it binds a predicted stem-loop structure on the incoming viral genomic RNA (identified by CLIP-Seq) and destabilizes it, attenuating infection at the earliest step of the replication cycle through an interferon-independent mechanism; this antiviral function is conserved between Drosophila and human cells.\",\n      \"method\": \"RNA interference screen, CLIP-Seq, viral infection assays with DDX56 depletion, immunofluorescence localization, Drosophila genetic knockdown\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — CLIP-Seq identifies specific RNA binding site, genetic knockdown with phenotypic readout replicated in two organisms (Drosophila and human cells), multiple orthogonal methods\",\n      \"pmids\": [\"33109765\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DDX56 interacts with the IAV NS1 protein (confirmed by yeast two-hybrid and co-immunoprecipitation in mammalian cells); DDX56 knockdown significantly reduces influenza A virus replication, indicating DDX56 is a positive host factor for IAV replication.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation in mammalian cells, colocalization by immunofluorescence, siRNA knockdown with viral replication assay\",\n      \"journal\": \"Genetics and molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP confirmed in mammalian cells, knockdown phenotype, single lab with two orthogonal binding assays\",\n      \"pmids\": [\"33749700\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DDX56 promotes EMCV replication by inhibiting IRF3 phosphorylation and nuclear translocation; mechanistically, DDX56 directly targets importin subunits KPNA3 and KPNA4 to block IRF3 nuclear import in the MDA5-triggered signaling cascade, thereby suppressing IFN-β production.\",\n      \"method\": \"Overexpression/knockdown viral replication assays, IRF3 phosphorylation and nuclear translocation assays, co-immunoprecipitation with KPNA3/KPNA4, IFN-β reporter assays\",\n      \"journal\": \"Veterinary microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with specific importin targets, nuclear translocation assays, knockdown phenotype, single lab with multiple methods\",\n      \"pmids\": [\"34922148\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Ddx56 is required for ribosome assembly in mouse embryonic stem cells (mESCs); knockout or knockdown of Ddx56 causes ribosome dysfunction and cell lethality; separately, Ddx56 interacts with the Oct4/Sox2 pluripotency complex by binding to Sox2 (confirmed by co-IP), and a C-terminal truncation (Ddx56 ΔC-ter) that does not affect ribosome assembly shows reduced Sox2 interaction and decreased mESC proliferation.\",\n      \"method\": \"Knockout/RNAi knockdown, polysome fractionation, co-immunoprecipitation, RNA sequencing, C-terminal truncation mutant analysis\",\n      \"journal\": \"Stem cell research & therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — polysome fractionation + Co-IP + domain-deletion mutant, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"32703285\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DDX56 promotes SqCLC cell growth and migration by post-transcriptionally upregulating Wnt pathway genes (CTNNB1, WNT2B); mechanistically, DDX56 facilitates degradation of primary miR-378a, leading to reduced mature miR-378a-3p and consequent derepression of WNT2B.\",\n      \"method\": \"siRNA knockdown and overexpression in vitro, xenograft in vivo, miRNA profiling, qRT-PCR for pri-miR-378a processing\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — functional knockdown/overexpression with specific miRNA processing readout, in vitro and in vivo, single lab\",\n      \"pmids\": [\"34446021\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In glioblastoma stem cells, DDX56 localizes to the nucleolus; loss of DDX56 in planarians causes dysregulation of ribosomal RNA expression and loss of nucleolar integrity prior to stem cell death, indicating a conserved role for DDX56 in nucleolar/ribosomal RNA biology in stem cells.\",\n      \"method\": \"Comparative genomics, RNAi knockdown in planarians, nucleolar integrity assays (microscopy), human GSC functional assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cross-species genetic knockdown with specific rRNA and nucleolar phenotype, replicated in multiple stem cell systems\",\n      \"pmids\": [\"33789112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DDX56 interacts with MECOM to promote mono-methylation of H3K9 (H3K9me1) on the MIST1 promoter, leading to enhanced MIST1 transcription and subsequent activation of PTEN/AKT signaling in HCC; ZEB1 transcriptionally activates DDX56 expression; DDX56 occupancy on the MIST1 promoter was confirmed by ChIP and EMSA.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), dual-luciferase reporter, in vitro/in vivo xenograft models, siRNA knockdown and overexpression\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP + EMSA + luciferase reporter with Co-IP, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"36168636\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DDX56 directly interacts with cGAS and promotes cGAS expression; this interaction enhances cGAS-STING-IFN-β signaling, including promoting IRF3 phosphorylation and nuclear translocation, thereby inhibiting pseudorabies virus (PRV) replication; knockdown of cGAS abrogates the antiviral and IFN-β-promoting effects of DDX56.\",\n      \"method\": \"Co-immunoprecipitation, overexpression/knockdown, IRF3 phosphorylation/translocation assays, cGAS knockdown epistasis, IFN-β reporter/quantification\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with epistasis (cGAS knockdown reversal), multiple functional readouts, single lab\",\n      \"pmids\": [\"36090064\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DDX56 promotes HCC EMT and cancer stemness through the MELK-FOXM1 signaling axis; DDX56 enhances MELK-mediated FOXM1 expression, regulating cancer stemness and malignant traits; knockdown of DDX56 in vivo reduced tumorigenicity and lung metastasis.\",\n      \"method\": \"siRNA knockdown and overexpression in vitro, in vivo tumor-bearing mouse model, EMT and stemness marker assays, MELK-FOXM1 pathway analysis\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, pathway-level phenotypic analysis without direct binding or biochemical demonstration of DDX56–MELK interaction mechanism\",\n      \"pmids\": [\"38827395\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DDX56 (NOH61) is a nucleolar DEAD-box RNA helicase with intrinsic ATPase activity that participates in 60S ribosomal subunit biogenesis (residing in 65S preribosomal particles), interacts with the Oct4/Sox2 pluripotency complex via Sox2 to support stem cell proliferation, and is co-opted by multiple RNA viruses: its helicase activity and interaction with WNV capsid protein are required for assembly of infectious WNV virions at ER assembly sites; it binds a stem-loop in the CHIKV genome to destabilize incoming viral RNA in an interferon-independent antiviral mechanism; and it suppresses type I interferon responses for FMDV and EMCV by inhibiting IRF3 phosphorylation/nuclear translocation through distinct mechanisms (interaction with FMDV 3A or targeting of importins KPNA3/KPNA4), while for PRV it enhances IFN-β through direct interaction with cGAS; in cancer contexts DDX56 promotes oncogenesis via H3K9 methylation-mediated transcriptional activation of MIST1/PTEN-AKT and miRNA-mediated post-transcriptional regulation of Wnt signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DDX56 (NOH61) is a nucleolar DEAD-box RNA helicase with polynucleotide-stimulated ATPase activity that functions in 60S ribosomal subunit biogenesis, residing in free nucleoplasmic 65S preribosomal particles and showing RNA-dependent nucleolar localization that is lost upon actinomycin D or RNase A treatment [#0]. This ribosome-assembly role is conserved across stem cell systems: Ddx56 is required for ribosome assembly and viability in mouse embryonic stem cells, where it also binds the Oct4/Sox2 pluripotency complex through Sox2 via its C-terminus to support proliferation independently of its ribosome function [#8], and its loss in planarians and human glioblastoma stem cells dysregulates rRNA and disrupts nucleolar integrity prior to stem cell death [#10]. DDX56 is repeatedly co-opted at the host–virus interface. For West Nile virus it relocalizes from the nucleolus to ER assembly sites, binds the capsid protein in an RNA-independent manner, and uses its helicase activity to support assembly of infectious virions without affecting RNA replication [#1, #2, #3]. In innate immunity DDX56 acts as both a proviral suppressor and an antiviral effector depending on context: it inhibits type I interferon signaling for FMDV by cooperating with the 3A protein to block IRF3 phosphorylation (requiring residue D166) [#4] and for EMCV by targeting importins KPNA3/KPNA4 to prevent IRF3 nuclear import [#7], yet it directly binds a stem-loop in incoming chikungunya virus genomic RNA to destabilize it in an interferon-independent manner [#5] and enhances cGAS-STING-IFN-β signaling against pseudorabies virus through direct interaction with cGAS [#12]. In cancer, DDX56 drives oncogenic transcriptional and post-transcriptional programs, partnering with MECOM to deposit H3K9me1 at the MIST1 promoter and activate PTEN-AKT signaling in HCC [#11] and promoting Wnt signaling by facilitating degradation of pri-miR-378a [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established the basic biochemical identity of DDX56 as a nucleolar DEAD-box ATPase and placed it in the ribosome biogenesis pathway, answering what kind of enzyme it is and where it acts.\",\n      \"evidence\": \"Recombinant ATPase assay, sucrose gradient sedimentation, biochemical fractionation and immunolocalization with actinomycin D/RNase A treatment in cultured cells\",\n      \"pmids\": [\"10749921\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"RNA substrate specificity of helicase activity not defined\", \"specific step in 60S maturation not pinpointed\", \"no structural model of oligomerization\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showed DDX56 is hijacked by West Nile virus as a host assembly factor, distinguishing its role from RNA replication and linking it to capsid via direct binding.\",\n      \"evidence\": \"Yeast two-hybrid, RNA-independent co-immunoprecipitation, siRNA knockdown and viral infectivity assays in infected cells\",\n      \"pmids\": [\"21411523\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"molecular mechanism by which DDX56 packages viral RNA unresolved\", \"did not address helicase requirement\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated that the helicase enzymatic activity and the capsid-binding interaction are functionally required for WNV virion assembly, moving from correlation to mechanism.\",\n      \"evidence\": \"Helicase-dead mutant and dominant-negative capsid-binding domain overexpression with infectivity readouts\",\n      \"pmids\": [\"22925334\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"RNA substrate acted upon during assembly unknown\", \"stoichiometry of capsid complex undefined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Refined the spatial model of WNV co-option, showing DDX56 and capsid colocalize at ER assembly sites while stable binding occurs in the nucleus, implying a transient cytoplasmic interaction.\",\n      \"evidence\": \"Super-resolution microscopy and fractionated co-immunoprecipitation\",\n      \"pmids\": [\"27821284\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"transient cytoplasmic interaction not directly captured biochemically\", \"trigger for nucleolar-to-ER relocalization unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Separated DDX56's ribosome-assembly role from a distinct pluripotency function in stem cells, using a domain mutant to dissociate the two activities.\",\n      \"evidence\": \"Knockout/RNAi, polysome fractionation, co-IP with Sox2 and C-terminal truncation mutant analysis in mESCs\",\n      \"pmids\": [\"32703285\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"mechanism of Sox2-DDX56 cooperation in proliferation undefined\", \"whether helicase activity contributes to pluripotency role unaddressed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed an intrinsic antiviral activity in which DDX56 directly recognizes and destabilizes viral genomic RNA, contrasting with its proviral roles.\",\n      \"evidence\": \"RNAi screen, CLIP-Seq mapping of a stem-loop binding site, infection assays in human and Drosophila cells\",\n      \"pmids\": [\"33109765\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"mechanism of RNA destabilization (helicase vs recruitment of nucleases) not resolved\", \"how DDX56 distinguishes viral from host RNA unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended DDX56's interferon-suppressive proviral function to EMCV through a specific block on IRF3 nuclear import via importin targeting.\",\n      \"evidence\": \"Co-IP with KPNA3/KPNA4, IRF3 phosphorylation/translocation assays, IFN-β reporter and knockdown in the MDA5 cascade\",\n      \"pmids\": [\"34922148\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"direct vs indirect KPNA binding not structurally defined\", \"relationship to FMDV mechanism not reconciled\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified DDX56 as a positive host factor for influenza A virus via interaction with NS1, broadening the range of viruses that exploit it.\",\n      \"evidence\": \"Yeast two-hybrid, mammalian co-IP, colocalization and siRNA knockdown with replication assay\",\n      \"pmids\": [\"33749700\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"functional consequence of NS1 binding mechanistically undefined\", \"single-lab interaction without reciprocal mapping\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connected DDX56 to oncogenic Wnt signaling through a post-transcriptional miRNA-processing mechanism, expanding its functional repertoire beyond viral and ribosomal roles.\",\n      \"evidence\": \"Knockdown/overexpression in vitro, xenograft, miRNA profiling and pri-miR-378a processing qRT-PCR in squamous cell lung carcinoma\",\n      \"pmids\": [\"34446021\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"direct binding of DDX56 to pri-miR-378a not demonstrated\", \"helicase requirement for miRNA degradation untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established conservation of DDX56's nucleolar/rRNA role in stem cell maintenance across species, tying ribosome biology to stem cell survival.\",\n      \"evidence\": \"Comparative genomics, planarian RNAi with nucleolar integrity and rRNA assays, human GSC functional assays\",\n      \"pmids\": [\"33789112\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"direct rRNA processing step affected not defined\", \"link between nucleolar disruption and cell death mechanistically unmapped\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined a chromatin-level oncogenic mechanism in which DDX56 partners with MECOM to deposit H3K9me1 and activate the MIST1/PTEN-AKT axis in HCC.\",\n      \"evidence\": \"Co-IP, ChIP, EMSA, dual-luciferase reporter and xenograft models with knockdown/overexpression\",\n      \"pmids\": [\"36168636\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"how an RNA helicase confers promoter occupancy/methyltransferase recruitment unclear\", \"direct vs MECOM-dependent DNA binding not separated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed a context-specific antiviral role in which DDX56 directly binds cGAS to enhance IFN-β signaling against PRV, contrasting with its IFN-suppressive activity in other infections.\",\n      \"evidence\": \"Co-IP, cGAS-knockdown epistasis, IRF3 phosphorylation/translocation and IFN-β assays\",\n      \"pmids\": [\"36090064\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"determinant of pro- vs anti-interferon switching across viruses unknown\", \"structural basis of cGAS interaction undefined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Proposed an additional oncogenic axis linking DDX56 to EMT and stemness via MELK-FOXM1 signaling in HCC.\",\n      \"evidence\": \"Knockdown/overexpression in vitro, in vivo metastasis model and EMT/stemness marker analysis\",\n      \"pmids\": [\"38827395\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"no direct DDX56-MELK binding or biochemical mechanism demonstrated\", \"pathway-level phenotype only\", \"relationship to other oncogenic axes unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"What determines whether DDX56 acts as a proviral interferon suppressor or an antiviral effector, and how its core helicase/ATPase activity is mechanistically deployed across ribosome assembly, viral RNA destabilization, and chromatin/miRNA regulation, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"unifying biochemical mechanism linking diverse roles absent\", \"no structural data for any partner interaction\", \"RNA substrate determinants undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 10]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [4, 7, 12]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [1, 5, 9, 11]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"WNV capsid\", \"Sox2\", \"FMDV 3A\", \"KPNA3\", \"KPNA4\", \"NS1\", \"cGAS\", \"MECOM\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":5,"faith_pct":80.0}}