{"gene":"RIOK1","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2010,"finding":"RioK1 is a stoichiometric component of the PRMT5 complex, binding PRMT5 in a mutually exclusive fashion with pICln. RioK1 and pICln both bind to a PRMT5-WD45/MEP50 core, forming distinct complexes. RioK1 acts as an adapter protein that recruits the RNA-binding protein nucleolin to the PRMT5 complex for its symmetrical arginine dimethylation.","method":"Biochemical purification, co-immunoprecipitation, stoichiometric complex analysis, in vitro methylation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — reciprocal Co-IP, biochemical reconstitution of complex, functional methylation assay, and identification of substrate recruitment mechanism in a single focused study","pmids":["21081503"],"is_preprint":false},{"year":2016,"finding":"RIOK1 is a co-complex protein of PRMT5 and its depletion creates a vulnerability in MTAP-deleted cancer cells, placing RIOK1 functionally downstream of MTA accumulation-mediated PRMT5 inhibition in the MAT2A/PRMT5/RIOK1 axis.","method":"shRNA screening, metabolomic profiling, biochemical methyltransferase inhibition assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — shRNA screen combined with biochemical profiling; RIOK1's direct mechanistic role in the axis is inferred from complex membership rather than direct enzymatic characterization","pmids":["27068473"],"is_preprint":false},{"year":2018,"finding":"RIOK1 is methylated at K411 by SETD7 methyltransferase; LSD1 reverses this methylation. The K411-methylated form is recognized by FBXO6 (via its FBA domain), leading to RIOK1 ubiquitination and degradation. CK2 phosphorylates RIOK1 at T410, which stabilizes RIOK1 by antagonizing K411 methylation and blocking FBXO6 recruitment. This methylation-phosphorylation switch regulates RIOK1 protein stability and tumor growth/metastasis.","method":"In vitro methylation/phosphorylation assays, mutagenesis (K411R), co-immunoprecipitation, ubiquitination assays, mouse xenograft models","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods including in vitro enzymatic assays, mutagenesis, co-IP for complex identification, and in vivo functional validation in a single rigorous study","pmids":["29384474"],"is_preprint":false},{"year":2018,"finding":"RIOK1 kinase activity is required for cancer cell survival irrespective of MTAP status. Using CRISPR/Cas9-generated analog-sensitive alleles, differential kinase activity requirement was NOT detected between MTAP-proficient and MTAP-deleted cells, contrasting with the differential PRMT5 dependency.","method":"CRISPR/Cas9 analog-sensitive kinase allele engineering, isogenic cell line comparison, chemical-genetic inhibition","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — rigorous chemical-genetic approach with isogenic lines; single lab but with orthogonal CRISPR and pharmacological methods","pmids":["29983885"],"is_preprint":false},{"year":2017,"finding":"RIOK1 knockdown in RAS-mutant cancer cells impairs proliferation and invasiveness, activates NF-κB signaling, and reduces expression of pro-invasive proteins Metadherin and Stathmin1. RIOK1 promotes cell cycle progression. These effects are specific to RAS-mutant cells and not observed in RAS-wildtype cells.","method":"shRNA knockdown, 3D culture, proteomics, NF-κB reporter assays, in vivo lung colonization assay","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — multiple orthogonal methods (knockdown, proteomics, in vivo), single lab, clear mechanistic pathway placement in RAS-mutant context","pmids":["28499923"],"is_preprint":false},{"year":2021,"finding":"The binding interface between RioK1 and the PRMT5 TIM barrel domain was mapped by peptide truncation and mutation studies. A consensus amino acid sequence GQF[D/E]DA[E/D] is involved in binding. Protein crystallography revealed that the RioK1-derived peptide interacts with a novel protein-protein interaction site on PRMT5, distinct from the pICln binding site.","method":"Peptide truncation and mutation studies, protein crystallography","journal":"Chembiochem : a European journal of chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional mutagenesis validation identifying novel PPI site; single lab but structural tier with mechanistic resolution","pmids":["33624332"],"is_preprint":false},{"year":2022,"finding":"RIOK1 phosphorylates G3BP2 at Thr226, increasing G3BP2 activity. RIOK1-mediated G3BP2 phosphorylation facilitates MDM2-mediated ubiquitination of p53, suppressing the p53 signaling pathway and contributing to radioresistance in colorectal cancer. RIOK1 and G3BP2 physically interact.","method":"Co-immunoprecipitation, in vitro kinase assay (phosphorylation at Thr226), ubiquitination assay, knockdown/inhibitor experiments in vitro and in vivo","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — direct kinase substrate identification with phosphosite mapping, co-IP for interaction, functional rescue, single lab","pmids":["35589951"],"is_preprint":false},{"year":2022,"finding":"NF90 (Nuclear Factor 90) specifically interacts with the PRMT5-WD45-RioK1 complex and is symmetrically dimethylated by PRMT5 within the RG-rich region of its C-terminus, establishing NF90 as a new substrate recruited via the RioK1 adaptor.","method":"Co-immunoprecipitation, in vitro/in vivo methylation assay, PRMT5 inhibitor treatment","journal":"Biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP for complex identification, methylation assay for substrate confirmation, single lab with two orthogonal methods","pmids":["36040368"],"is_preprint":false},{"year":2018,"finding":"In C. elegans, riok-1 acts upstream of the p38 MAPK/pmk-1 pathway as a negative regulator (suppressor) of innate immune signaling. Genetic epistasis placed riok-1 downstream of skn-1 (a p38 MAPK transcription factor), suggesting a negative feedback loop: SKN-1 → RIOK-1 ⊣ p38 MAPK/PMK-1.","method":"RNAi knockdown, genetic epistasis analysis, quantitative RT-PCR, infection resistance assays","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with multiple pathway components, C. elegans ortholog study with functional pathway placement","pmids":["29719537"],"is_preprint":false},{"year":2014,"finding":"In C. elegans, depletion of riok-1 (ortholog of mammalian RIOK1) suppresses the multi-vulva phenotype caused by oncogenic Ras/Raf signaling, placing riok-1 as a modulator of the Ras signaling pathway.","method":"RNAi screen in C. elegans, multi-vulva phenotype assay, promoter-GFP expression analysis","journal":"Gene expression patterns : GEP","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis via RNAi suppressor screen in C. elegans ortholog, single lab","pmids":["24929033"],"is_preprint":false},{"year":2024,"finding":"RIOK1 forms a trimeric complex with SPC25 and MYH9, where SPC25 acts as a scaffold. Within this complex, RIOK1 phosphorylates MYH9 at Ser1943. This phosphorylation causes MYH9 to disengage from the cytoskeleton and accumulate in the nucleus, potentiating CTNNB1 transcription and Wnt/β-catenin signaling activation, promoting cancer stem cell phenotypes and platinum resistance.","method":"Co-immunoprecipitation, in vitro kinase assay (phosphorylation at Ser1943), mutagenesis, nuclear fractionation, competitive inhibitory peptide (CBP1), patient-derived organoids","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct kinase substrate identification with phosphosite mutagenesis, complex reconstitution by Co-IP, subcellular fractionation tied to functional outcome, multiple orthogonal methods and in vivo/organoid validation","pmids":["39488790"],"is_preprint":false},{"year":2025,"finding":"RIOK1 undergoes liquid-liquid phase separation and incorporates IGF2BP1 and G3BP1 into stress granules. These RIOK1-positive stress granules sequester PTEN mRNA, reducing its translation, thereby activating the pentose phosphate pathway and facilitating stress resolution and cytoprotection against tyrosine kinase inhibitors in hepatocellular carcinoma.","method":"Phase separation assays, stress granule immunofluorescence, mRNA translation assays, RNA immunoprecipitation, metabolic profiling, in vitro and in vivo TKI resistance models","journal":"Nature cancer","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — phase separation and stress granule formation demonstrated experimentally, mRNA sequestration shown, but single lab; mechanistic details on phase separation domain not fully characterized in abstract","pmids":["40467995"],"is_preprint":false},{"year":2025,"finding":"RIOK1 interacts with YBX1 and induces phosphorylation of YBX1 at Ser165, promoting nuclear localization of YBX1, which in turn activates the JAK2/STAT3 pathway and increases lenvatinib resistance in hepatocellular carcinoma cells.","method":"Co-immunoprecipitation, phosphorylation site identification, nuclear fractionation, knockdown/overexpression functional assays, mouse xenograft","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP for interaction, phosphosite identified, functional rescue experiments, subcellular localization linked to pathway activation; single lab","pmids":["41354180"],"is_preprint":false},{"year":2023,"finding":"RIOK1 is identified as a downstream target gene of the c-myc/E2F transcription factors in prostate cancer. A dominant-negative RIOK1-D324A mutant reduces PCa cell proliferation, and toyocamycin treatment (RIOK1 biochemical inhibitor) causes rapid decreases in RIOK1 protein, total rRNA content, and shifts the 28S/18S rRNA ratio, consistent with a role in ribosome biogenesis.","method":"Chromatin immunoprecipitation/transcription factor target analysis, dominant-negative mutagenesis (D324A), rRNA quantification, pharmacological inhibition with toyocamycin","journal":"The American journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — dominant-negative mutant and pharmacological inhibition with rRNA readouts; transcription factor regulation by ChIP/reporter; single lab","pmids":["37301535"],"is_preprint":false}],"current_model":"RIOK1 is an atypical serine/threonine kinase/ATPase that functions as a substrate-recruiting adapter within the PRMT5-WD45/MEP50 complex (competing with pICln) to recruit substrates such as nucleolin and NF90 for symmetrical arginine dimethylation; it also phosphorylates substrates including G3BP2 (T226), MYH9 (S1943), and YBX1 (S165) to regulate p53 stability, Wnt/β-catenin signaling, and JAK2/STAT3 pathway activation respectively; its own stability is controlled by a SETD7/LSD1 methylation–CK2 phosphorylation switch at residues T410/K411 that gates FBXO6-mediated ubiquitination; and it can undergo liquid-liquid phase separation to form stress granules that sequester PTEN mRNA, suppressing PTEN translation and activating downstream oncogenic pathways."},"narrative":{"mechanistic_narrative":"RIOK1 is an atypical kinase/ATPase that operates both as a substrate-recruiting adapter within the PRMT5 methylosome and as an active protein kinase driving oncogenic signaling [PMID:21081503, PMID:35589951]. As a stoichiometric component of the PRMT5-WD45/MEP50 core, RIOK1 binds PRMT5 mutually exclusively with pICln through a distinct interface on the PRMT5 TIM-barrel domain (consensus GQF[D/E]DA[E/D]), recruiting RNA-binding substrates such as nucleolin and NF90 for symmetrical arginine dimethylation [PMID:21081503, PMID:33624332, PMID:36040368]; consistent with this methylosome role, RIOK1 depletion is selectively lethal in MTAP-deleted cancer cells within the MAT2A/PRMT5/RIOK1 axis, and its kinase activity supports cell survival and ribosome biogenesis [PMID:27068473, PMID:29983885, PMID:37301535]. As a kinase, RIOK1 phosphorylates G3BP2 at Thr226 to promote MDM2-mediated p53 degradation and radioresistance, MYH9 at Ser1943 (within a SPC25-scaffolded trimer) to drive nuclear MYH9 accumulation and Wnt/β-catenin activation, and YBX1 at Ser165 to promote its nuclear localization and JAK2/STAT3 activation [PMID:35589951, PMID:39488790, PMID:41354180]. RIOK1 also undergoes liquid-liquid phase separation, nucleating stress granules with IGF2BP1 and G3BP1 that sequester PTEN mRNA and suppress its translation [PMID:40467995]. RIOK1 protein stability is gated by a methylation–phosphorylation switch: SETD7 methylates K411 (reversed by LSD1) to license FBXO6-mediated ubiquitination, while CK2 phosphorylation of T410 antagonizes K411 methylation and stabilizes the protein [PMID:29384474]. Across model systems, RIOK1 acts as a modulator of Ras signaling and innate immune signaling [PMID:24929033, PMID:29719537].","teleology":[{"year":2010,"claim":"Established RIOK1's first defined molecular role: not as a free kinase but as a dedicated adapter that loads specific RNA-binding substrates onto the PRMT5 arginine methyltransferase complex.","evidence":"Biochemical purification, reciprocal co-IP, stoichiometric complex analysis, and in vitro methylation assay of nucleolin","pmids":["21081503"],"confidence":"High","gaps":["Did not define how RIOK1 selects which substrates to recruit","Relationship between adapter function and RIOK1's catalytic activity unresolved"]},{"year":2014,"claim":"Placed the RIOK1 ortholog genetically within oncogenic Ras/Raf signaling, indicating a conserved role in proliferative signaling beyond the methylosome.","evidence":"RNAi suppressor screen of the multi-vulva phenotype in C. elegans","pmids":["24929033"],"confidence":"Medium","gaps":["Ortholog genetics do not define the molecular step in the Ras pathway","No mammalian biochemical mechanism shown"]},{"year":2016,"claim":"Connected RIOK1 to a therapeutic vulnerability, showing its depletion is selectively lethal in MTAP-deleted cells downstream of PRMT5 inhibition.","evidence":"shRNA screening with metabolomic profiling and methyltransferase inhibition assays","pmids":["27068473"],"confidence":"Medium","gaps":["RIOK1's direct mechanistic contribution inferred from complex membership, not enzymatic characterization","Did not test whether kinase activity is required"]},{"year":2017,"claim":"Defined a RAS-mutant-selective requirement for RIOK1 in proliferation and invasion, linking it to NF-κB signaling and pro-invasive effectors.","evidence":"shRNA knockdown, 3D culture, proteomics, NF-κB reporter, and in vivo lung colonization in RAS-mutant cells","pmids":["28499923"],"confidence":"Medium","gaps":["Direct kinase substrates in this context not identified","Mechanism linking RIOK1 to NF-κB unresolved"]},{"year":2018,"claim":"Resolved how RIOK1 protein levels are controlled, defining a SETD7/LSD1 methylation–CK2 phosphorylation switch at T410/K411 that gates FBXO6-mediated degradation.","evidence":"In vitro methylation/phosphorylation assays, K411R mutagenesis, ubiquitination assays, and mouse xenografts","pmids":["29384474"],"confidence":"High","gaps":["Upstream signals controlling SETD7/LSD1/CK2 activity on RIOK1 not defined","Whether stability switch couples to specific RIOK1 functions unknown"]},{"year":2018,"claim":"Distinguished RIOK1's kinase requirement from its methylosome role, showing kinase activity is needed for survival regardless of MTAP status.","evidence":"CRISPR analog-sensitive kinase alleles with isogenic cell comparison and chemical-genetic inhibition","pmids":["29983885"],"confidence":"Medium","gaps":["The MTAP-independent kinase substrates were not identified here","Single-lab chemical-genetic system"]},{"year":2018,"claim":"Identified a conserved negative-feedback role for the RIOK1 ortholog in innate immunity, acting downstream of SKN-1 to suppress p38 MAPK/PMK-1 signaling.","evidence":"RNAi, genetic epistasis, qRT-PCR, and infection assays in C. elegans","pmids":["29719537"],"confidence":"Medium","gaps":["Molecular mechanism of p38 suppression not defined","Mammalian relevance of immune role untested"]},{"year":2021,"claim":"Provided structural resolution of the RIOK1–PRMT5 interaction, mapping a consensus motif binding a novel PRMT5 site distinct from pICln.","evidence":"Peptide truncation/mutation studies and protein crystallography of the RioK1 peptide-PRMT5 complex","pmids":["33624332"],"confidence":"High","gaps":["Structure of full-length RIOK1 within the complex not determined","How the interface switches with pICln dynamically unresolved"]},{"year":2022,"claim":"Established RIOK1 as a direct kinase against G3BP2 at Thr226, linking its catalytic activity to p53 suppression and radioresistance.","evidence":"Co-IP, in vitro kinase assay with phosphosite mapping, ubiquitination assays, and in vitro/in vivo functional tests in colorectal cancer","pmids":["35589951"],"confidence":"Medium","gaps":["Mechanism linking G3BP2-T226 to MDM2 activity not fully resolved","Single-lab substrate identification"]},{"year":2022,"claim":"Expanded the RIOK1-adapter substrate repertoire by identifying NF90 as a PRMT5 substrate recruited via the RioK1 complex.","evidence":"Co-IP, in vitro/in vivo methylation assay, and PRMT5 inhibitor treatment","pmids":["36040368"],"confidence":"Medium","gaps":["Functional consequence of NF90 methylation not defined","Recruitment determinants not mapped"]},{"year":2023,"claim":"Positioned RIOK1 as a c-myc/E2F transcriptional target with a ribosome biogenesis function in prostate cancer.","evidence":"Transcription factor target analysis, dominant-negative D324A mutant, rRNA quantification, and toyocamycin inhibition","pmids":["37301535"],"confidence":"Medium","gaps":["Direct biochemical role of RIOK1 in rRNA processing not defined","rRNA changes could be indirect via toyocamycin"]},{"year":2024,"claim":"Defined a SPC25-scaffolded RIOK1–MYH9 trimer in which RIOK1 phosphorylates MYH9-S1943 to drive nuclear MYH9 and Wnt/β-catenin-mediated stemness and platinum resistance.","evidence":"Co-IP, in vitro kinase assay with phosphosite mutagenesis, nuclear fractionation, inhibitory peptide, and patient-derived organoids","pmids":["39488790"],"confidence":"High","gaps":["How SPC25 scaffolding selects MYH9 for phosphorylation not detailed","Link between cytoskeletal disengagement and CTNNB1 transcription mechanistically incomplete"]},{"year":2025,"claim":"Revealed a non-catalytic biophysical function: RIOK1 undergoes phase separation to build PTEN-mRNA-sequestering stress granules that reprogram metabolism and confer TKI resistance.","evidence":"Phase separation assays, stress granule immunofluorescence, RNA-IP, translation and metabolic profiling, and in vivo TKI resistance models in HCC","pmids":["40467995"],"confidence":"Medium","gaps":["The RIOK1 domain/region driving phase separation not characterized","Selectivity for PTEN mRNA mechanism unresolved"]},{"year":2025,"claim":"Added YBX1-S165 as a RIOK1 kinase substrate, coupling its catalytic activity to YBX1 nuclear localization and JAK2/STAT3-driven lenvatinib resistance.","evidence":"Co-IP, phosphosite identification, nuclear fractionation, functional rescue, and mouse xenograft","pmids":["41354180"],"confidence":"Medium","gaps":["How S165 phosphorylation drives YBX1 nuclear import not defined","Single-lab substrate identification"]},{"year":null,"claim":"It remains unresolved how RIOK1's distinct activities — methylosome adapter, ATPase/kinase toward diverse substrates, ribosome biogenesis factor, and phase-separation scaffold — are coordinated or selected within a single cell.","evidence":"No integrative study reconciling adapter versus kinase versus condensate functions in the timeline","pmids":[],"confidence":"Low","gaps":["No unified structural/biochemical model linking the functions","Substrate selectivity determinants for the kinase activity undefined","Conditions favoring phase separation versus complex assembly unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[6,10,12]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,5,7]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[11]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[10,12]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[11]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,7]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[10,12]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[2]}],"complexes":["PRMT5-WD45/MEP50 methylosome","RIOK1-SPC25-MYH9 trimer","RIOK1-positive stress granules"],"partners":["PRMT5","WD45/MEP50","FBXO6","G3BP2","SPC25","MYH9","YBX1","IGF2BP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BRS2","full_name":"Serine/threonine-protein kinase RIO1","aliases":["RIO kinase 1"],"length_aa":568,"mass_kda":65.6,"function":"Involved in the final steps of cytoplasmic maturation of the 40S ribosomal subunit. Involved in processing of 18S-E pre-rRNA to the mature 18S rRNA. Required for the recycling of NOB1 and PNO1 from the late 40S precursor (PubMed:22072790). The association with the very late 40S subunit intermediate may involve a translation-like checkpoint point cycle preceeding the binding to the 60S ribosomal subunit (By similarity). Despite the protein kinase domain is proposed to act predominantly as an ATPase (By similarity). The catalytic activity regulates its dynamic association with the 40S subunit (By similarity). In addition to its role in ribosomal biogenesis acts as an adapter protein by recruiting NCL/nucleolin the to PRMT5 complex for its symmetrical methylation (PubMed:21081503)","subcellular_location":"Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/Q9BRS2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RIOK1","classification":"Common Essential","n_dependent_lines":1164,"n_total_lines":1208,"dependency_fraction":0.9635761589403974},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000124784","cell_line_id":"CID001256","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":2}],"interactors":[{"gene":"CLNS1A","stoichiometry":0.2},{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"RPS15","stoichiometry":0.2},{"gene":"PRMT5","stoichiometry":0.2},{"gene":"NCL","stoichiometry":0.2},{"gene":"WDR77","stoichiometry":0.2},{"gene":"PNO1","stoichiometry":0.2},{"gene":"DDX31","stoichiometry":0.2},{"gene":"EIF1AD","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001256","total_profiled":1310},"omim":[{"mim_id":"620074","title":"LTV1 RIBOSOME BIOGENESIS FACTOR; LTV1","url":"https://www.omim.org/entry/620074"},{"mim_id":"618710","title":"PARTNER OF NOB1; PNO1","url":"https://www.omim.org/entry/618710"},{"mim_id":"617754","title":"RIO KINASE 2; RIOK2","url":"https://www.omim.org/entry/617754"},{"mim_id":"617753","title":"RIO KINASE 1; RIOK1","url":"https://www.omim.org/entry/617753"},{"mim_id":"617723","title":"RIBOSOMAL RNA-PROCESSING 12; RRP12","url":"https://www.omim.org/entry/617723"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RIOK1"},"hgnc":{"alias_symbol":["AD034","FLJ30006","bA288G3.1","RRP10"],"prev_symbol":[]},"alphafold":{"accession":"Q9BRS2","domains":[{"cath_id":"3.30.200.20","chopping":"115-127_136-283","consensus_level":"medium","plddt":79.1561,"start":115,"end":283},{"cath_id":"1.10.510.10","chopping":"288-492","consensus_level":"medium","plddt":84.8323,"start":288,"end":492}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BRS2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BRS2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BRS2-F1-predicted_aligned_error_v6.png","plddt_mean":68.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RIOK1","jax_strain_url":"https://www.jax.org/strain/search?query=RIOK1"},"sequence":{"accession":"Q9BRS2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BRS2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BRS2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BRS2"}},"corpus_meta":[{"pmid":"27068473","id":"PMC_27068473","title":"MTAP Deletions in Cancer Create Vulnerability to Targeting of the MAT2A/PRMT5/RIOK1 Axis.","date":"2016","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27068473","citation_count":364,"is_preprint":false},{"pmid":"21081503","id":"PMC_21081503","title":"RioK1, a new interactor of protein arginine methyltransferase 5 (PRMT5), competes with pICln for binding and modulates PRMT5 complex composition and substrate specificity.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21081503","citation_count":131,"is_preprint":false},{"pmid":"29384474","id":"PMC_29384474","title":"Targeting posttranslational modifications of RIOK1 inhibits the progression of colorectal and gastric cancers.","date":"2018","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/29384474","citation_count":63,"is_preprint":false},{"pmid":"28499923","id":"PMC_28499923","title":"The Atypical Kinase RIOK1 Promotes Tumor Growth and Invasive Behavior.","date":"2017","source":"EBioMedicine","url":"https://pubmed.ncbi.nlm.nih.gov/28499923","citation_count":43,"is_preprint":false},{"pmid":"35589951","id":"PMC_35589951","title":"RIOK1 mediates p53 degradation and radioresistance in colorectal cancer through phosphorylation of G3BP2.","date":"2022","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/35589951","citation_count":33,"is_preprint":false},{"pmid":"40467995","id":"PMC_40467995","title":"RIOK1 phase separation restricts PTEN translation via stress granules activating tumor growth in hepatocellular carcinoma.","date":"2025","source":"Nature cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40467995","citation_count":23,"is_preprint":false},{"pmid":"33624332","id":"PMC_33624332","title":"Biochemical Investigation of the Interaction of pICln, RioK1 and COPR5 with the PRMT5-MEP50 Complex.","date":"2021","source":"Chembiochem : a European journal of chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/33624332","citation_count":22,"is_preprint":false},{"pmid":"32599985","id":"PMC_32599985","title":"Elevated Expression of RIOK1 Is Correlated with Breast Cancer Hormone Receptor Status and Promotes Cancer Progression.","date":"2020","source":"Cancer research and treatment","url":"https://pubmed.ncbi.nlm.nih.gov/32599985","citation_count":15,"is_preprint":false},{"pmid":"29719537","id":"PMC_29719537","title":"RIOK-1 Is a Suppressor of the p38 MAPK Innate Immune Pathway in Caenorhabditis elegans.","date":"2018","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29719537","citation_count":14,"is_preprint":false},{"pmid":"39488790","id":"PMC_39488790","title":"Targeting the SPC25/RIOK1/MYH9 Axis to Overcome Tumor Stemness and Platinum Resistance in Epithelial Ovarian Cancer.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, 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Protein Kinase/ATPase RIOK1 Is Up-Regulated via the c-myc/E2F Transcription Factor Axis in Prostate Cancer.","date":"2023","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/37301535","citation_count":10,"is_preprint":false},{"pmid":"37935656","id":"PMC_37935656","title":"The RioK1 network determines p53 activity at multiple levels.","date":"2023","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/37935656","citation_count":7,"is_preprint":false},{"pmid":"37298928","id":"PMC_37298928","title":"Riok1, A Novel Potential Target in MSI-High p53 Mutant Colorectal Cancer Cells.","date":"2023","source":"Molecules (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/37298928","citation_count":6,"is_preprint":false},{"pmid":"40982243","id":"PMC_40982243","title":"Phospho-Regulatory Network of the Right Open Reading Frame Kinase 1 (RIOK1), Its Functional Relevance, and Cancer Treatment Prospects.","date":"2025","source":"Omics : a 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RioK1 and pICln both bind to a PRMT5-WD45/MEP50 core, forming distinct complexes. RioK1 acts as an adapter protein that recruits the RNA-binding protein nucleolin to the PRMT5 complex for its symmetrical arginine dimethylation.\",\n      \"method\": \"Biochemical purification, co-immunoprecipitation, stoichiometric complex analysis, in vitro methylation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — reciprocal Co-IP, biochemical reconstitution of complex, functional methylation assay, and identification of substrate recruitment mechanism in a single focused study\",\n      \"pmids\": [\"21081503\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RIOK1 is a co-complex protein of PRMT5 and its depletion creates a vulnerability in MTAP-deleted cancer cells, placing RIOK1 functionally downstream of MTA accumulation-mediated PRMT5 inhibition in the MAT2A/PRMT5/RIOK1 axis.\",\n      \"method\": \"shRNA screening, metabolomic profiling, biochemical methyltransferase inhibition assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — shRNA screen combined with biochemical profiling; RIOK1's direct mechanistic role in the axis is inferred from complex membership rather than direct enzymatic characterization\",\n      \"pmids\": [\"27068473\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RIOK1 is methylated at K411 by SETD7 methyltransferase; LSD1 reverses this methylation. The K411-methylated form is recognized by FBXO6 (via its FBA domain), leading to RIOK1 ubiquitination and degradation. CK2 phosphorylates RIOK1 at T410, which stabilizes RIOK1 by antagonizing K411 methylation and blocking FBXO6 recruitment. This methylation-phosphorylation switch regulates RIOK1 protein stability and tumor growth/metastasis.\",\n      \"method\": \"In vitro methylation/phosphorylation assays, mutagenesis (K411R), co-immunoprecipitation, ubiquitination assays, mouse xenograft models\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods including in vitro enzymatic assays, mutagenesis, co-IP for complex identification, and in vivo functional validation in a single rigorous study\",\n      \"pmids\": [\"29384474\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RIOK1 kinase activity is required for cancer cell survival irrespective of MTAP status. Using CRISPR/Cas9-generated analog-sensitive alleles, differential kinase activity requirement was NOT detected between MTAP-proficient and MTAP-deleted cells, contrasting with the differential PRMT5 dependency.\",\n      \"method\": \"CRISPR/Cas9 analog-sensitive kinase allele engineering, isogenic cell line comparison, chemical-genetic inhibition\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — rigorous chemical-genetic approach with isogenic lines; single lab but with orthogonal CRISPR and pharmacological methods\",\n      \"pmids\": [\"29983885\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RIOK1 knockdown in RAS-mutant cancer cells impairs proliferation and invasiveness, activates NF-κB signaling, and reduces expression of pro-invasive proteins Metadherin and Stathmin1. RIOK1 promotes cell cycle progression. These effects are specific to RAS-mutant cells and not observed in RAS-wildtype cells.\",\n      \"method\": \"shRNA knockdown, 3D culture, proteomics, NF-κB reporter assays, in vivo lung colonization assay\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — multiple orthogonal methods (knockdown, proteomics, in vivo), single lab, clear mechanistic pathway placement in RAS-mutant context\",\n      \"pmids\": [\"28499923\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The binding interface between RioK1 and the PRMT5 TIM barrel domain was mapped by peptide truncation and mutation studies. A consensus amino acid sequence GQF[D/E]DA[E/D] is involved in binding. Protein crystallography revealed that the RioK1-derived peptide interacts with a novel protein-protein interaction site on PRMT5, distinct from the pICln binding site.\",\n      \"method\": \"Peptide truncation and mutation studies, protein crystallography\",\n      \"journal\": \"Chembiochem : a European journal of chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional mutagenesis validation identifying novel PPI site; single lab but structural tier with mechanistic resolution\",\n      \"pmids\": [\"33624332\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RIOK1 phosphorylates G3BP2 at Thr226, increasing G3BP2 activity. RIOK1-mediated G3BP2 phosphorylation facilitates MDM2-mediated ubiquitination of p53, suppressing the p53 signaling pathway and contributing to radioresistance in colorectal cancer. RIOK1 and G3BP2 physically interact.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assay (phosphorylation at Thr226), ubiquitination assay, knockdown/inhibitor experiments in vitro and in vivo\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — direct kinase substrate identification with phosphosite mapping, co-IP for interaction, functional rescue, single lab\",\n      \"pmids\": [\"35589951\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NF90 (Nuclear Factor 90) specifically interacts with the PRMT5-WD45-RioK1 complex and is symmetrically dimethylated by PRMT5 within the RG-rich region of its C-terminus, establishing NF90 as a new substrate recruited via the RioK1 adaptor.\",\n      \"method\": \"Co-immunoprecipitation, in vitro/in vivo methylation assay, PRMT5 inhibitor treatment\",\n      \"journal\": \"Biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP for complex identification, methylation assay for substrate confirmation, single lab with two orthogonal methods\",\n      \"pmids\": [\"36040368\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In C. elegans, riok-1 acts upstream of the p38 MAPK/pmk-1 pathway as a negative regulator (suppressor) of innate immune signaling. Genetic epistasis placed riok-1 downstream of skn-1 (a p38 MAPK transcription factor), suggesting a negative feedback loop: SKN-1 → RIOK-1 ⊣ p38 MAPK/PMK-1.\",\n      \"method\": \"RNAi knockdown, genetic epistasis analysis, quantitative RT-PCR, infection resistance assays\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with multiple pathway components, C. elegans ortholog study with functional pathway placement\",\n      \"pmids\": [\"29719537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In C. elegans, depletion of riok-1 (ortholog of mammalian RIOK1) suppresses the multi-vulva phenotype caused by oncogenic Ras/Raf signaling, placing riok-1 as a modulator of the Ras signaling pathway.\",\n      \"method\": \"RNAi screen in C. elegans, multi-vulva phenotype assay, promoter-GFP expression analysis\",\n      \"journal\": \"Gene expression patterns : GEP\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis via RNAi suppressor screen in C. elegans ortholog, single lab\",\n      \"pmids\": [\"24929033\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RIOK1 forms a trimeric complex with SPC25 and MYH9, where SPC25 acts as a scaffold. Within this complex, RIOK1 phosphorylates MYH9 at Ser1943. This phosphorylation causes MYH9 to disengage from the cytoskeleton and accumulate in the nucleus, potentiating CTNNB1 transcription and Wnt/β-catenin signaling activation, promoting cancer stem cell phenotypes and platinum resistance.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assay (phosphorylation at Ser1943), mutagenesis, nuclear fractionation, competitive inhibitory peptide (CBP1), patient-derived organoids\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct kinase substrate identification with phosphosite mutagenesis, complex reconstitution by Co-IP, subcellular fractionation tied to functional outcome, multiple orthogonal methods and in vivo/organoid validation\",\n      \"pmids\": [\"39488790\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RIOK1 undergoes liquid-liquid phase separation and incorporates IGF2BP1 and G3BP1 into stress granules. These RIOK1-positive stress granules sequester PTEN mRNA, reducing its translation, thereby activating the pentose phosphate pathway and facilitating stress resolution and cytoprotection against tyrosine kinase inhibitors in hepatocellular carcinoma.\",\n      \"method\": \"Phase separation assays, stress granule immunofluorescence, mRNA translation assays, RNA immunoprecipitation, metabolic profiling, in vitro and in vivo TKI resistance models\",\n      \"journal\": \"Nature cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — phase separation and stress granule formation demonstrated experimentally, mRNA sequestration shown, but single lab; mechanistic details on phase separation domain not fully characterized in abstract\",\n      \"pmids\": [\"40467995\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RIOK1 interacts with YBX1 and induces phosphorylation of YBX1 at Ser165, promoting nuclear localization of YBX1, which in turn activates the JAK2/STAT3 pathway and increases lenvatinib resistance in hepatocellular carcinoma cells.\",\n      \"method\": \"Co-immunoprecipitation, phosphorylation site identification, nuclear fractionation, knockdown/overexpression functional assays, mouse xenograft\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP for interaction, phosphosite identified, functional rescue experiments, subcellular localization linked to pathway activation; single lab\",\n      \"pmids\": [\"41354180\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RIOK1 is identified as a downstream target gene of the c-myc/E2F transcription factors in prostate cancer. A dominant-negative RIOK1-D324A mutant reduces PCa cell proliferation, and toyocamycin treatment (RIOK1 biochemical inhibitor) causes rapid decreases in RIOK1 protein, total rRNA content, and shifts the 28S/18S rRNA ratio, consistent with a role in ribosome biogenesis.\",\n      \"method\": \"Chromatin immunoprecipitation/transcription factor target analysis, dominant-negative mutagenesis (D324A), rRNA quantification, pharmacological inhibition with toyocamycin\",\n      \"journal\": \"The American journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — dominant-negative mutant and pharmacological inhibition with rRNA readouts; transcription factor regulation by ChIP/reporter; single lab\",\n      \"pmids\": [\"37301535\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RIOK1 is an atypical serine/threonine kinase/ATPase that functions as a substrate-recruiting adapter within the PRMT5-WD45/MEP50 complex (competing with pICln) to recruit substrates such as nucleolin and NF90 for symmetrical arginine dimethylation; it also phosphorylates substrates including G3BP2 (T226), MYH9 (S1943), and YBX1 (S165) to regulate p53 stability, Wnt/β-catenin signaling, and JAK2/STAT3 pathway activation respectively; its own stability is controlled by a SETD7/LSD1 methylation–CK2 phosphorylation switch at residues T410/K411 that gates FBXO6-mediated ubiquitination; and it can undergo liquid-liquid phase separation to form stress granules that sequester PTEN mRNA, suppressing PTEN translation and activating downstream oncogenic pathways.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RIOK1 is an atypical kinase/ATPase that operates both as a substrate-recruiting adapter within the PRMT5 methylosome and as an active protein kinase driving oncogenic signaling [#0, #6]. As a stoichiometric component of the PRMT5-WD45/MEP50 core, RIOK1 binds PRMT5 mutually exclusively with pICln through a distinct interface on the PRMT5 TIM-barrel domain (consensus GQF[D/E]DA[E/D]), recruiting RNA-binding substrates such as nucleolin and NF90 for symmetrical arginine dimethylation [#0, #5, #7]; consistent with this methylosome role, RIOK1 depletion is selectively lethal in MTAP-deleted cancer cells within the MAT2A/PRMT5/RIOK1 axis, and its kinase activity supports cell survival and ribosome biogenesis [#1, #3, #13]. As a kinase, RIOK1 phosphorylates G3BP2 at Thr226 to promote MDM2-mediated p53 degradation and radioresistance, MYH9 at Ser1943 (within a SPC25-scaffolded trimer) to drive nuclear MYH9 accumulation and Wnt/\\u03b2-catenin activation, and YBX1 at Ser165 to promote its nuclear localization and JAK2/STAT3 activation [#6, #10, #12]. RIOK1 also undergoes liquid-liquid phase separation, nucleating stress granules with IGF2BP1 and G3BP1 that sequester PTEN mRNA and suppress its translation [#11]. RIOK1 protein stability is gated by a methylation\\u2013phosphorylation switch: SETD7 methylates K411 (reversed by LSD1) to license FBXO6-mediated ubiquitination, while CK2 phosphorylation of T410 antagonizes K411 methylation and stabilizes the protein [#2]. Across model systems, RIOK1 acts as a modulator of Ras signaling and innate immune signaling [#9, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established RIOK1's first defined molecular role: not as a free kinase but as a dedicated adapter that loads specific RNA-binding substrates onto the PRMT5 arginine methyltransferase complex.\",\n      \"evidence\": \"Biochemical purification, reciprocal co-IP, stoichiometric complex analysis, and in vitro methylation assay of nucleolin\",\n      \"pmids\": [\"21081503\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define how RIOK1 selects which substrates to recruit\", \"Relationship between adapter function and RIOK1's catalytic activity unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Placed the RIOK1 ortholog genetically within oncogenic Ras/Raf signaling, indicating a conserved role in proliferative signaling beyond the methylosome.\",\n      \"evidence\": \"RNAi suppressor screen of the multi-vulva phenotype in C. elegans\",\n      \"pmids\": [\"24929033\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ortholog genetics do not define the molecular step in the Ras pathway\", \"No mammalian biochemical mechanism shown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Connected RIOK1 to a therapeutic vulnerability, showing its depletion is selectively lethal in MTAP-deleted cells downstream of PRMT5 inhibition.\",\n      \"evidence\": \"shRNA screening with metabolomic profiling and methyltransferase inhibition assays\",\n      \"pmids\": [\"27068473\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"RIOK1's direct mechanistic contribution inferred from complex membership, not enzymatic characterization\", \"Did not test whether kinase activity is required\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined a RAS-mutant-selective requirement for RIOK1 in proliferation and invasion, linking it to NF-\\u03baB signaling and pro-invasive effectors.\",\n      \"evidence\": \"shRNA knockdown, 3D culture, proteomics, NF-\\u03baB reporter, and in vivo lung colonization in RAS-mutant cells\",\n      \"pmids\": [\"28499923\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct kinase substrates in this context not identified\", \"Mechanism linking RIOK1 to NF-\\u03baB unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Resolved how RIOK1 protein levels are controlled, defining a SETD7/LSD1 methylation\\u2013CK2 phosphorylation switch at T410/K411 that gates FBXO6-mediated degradation.\",\n      \"evidence\": \"In vitro methylation/phosphorylation assays, K411R mutagenesis, ubiquitination assays, and mouse xenografts\",\n      \"pmids\": [\"29384474\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Upstream signals controlling SETD7/LSD1/CK2 activity on RIOK1 not defined\", \"Whether stability switch couples to specific RIOK1 functions unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Distinguished RIOK1's kinase requirement from its methylosome role, showing kinase activity is needed for survival regardless of MTAP status.\",\n      \"evidence\": \"CRISPR analog-sensitive kinase alleles with isogenic cell comparison and chemical-genetic inhibition\",\n      \"pmids\": [\"29983885\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The MTAP-independent kinase substrates were not identified here\", \"Single-lab chemical-genetic system\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified a conserved negative-feedback role for the RIOK1 ortholog in innate immunity, acting downstream of SKN-1 to suppress p38 MAPK/PMK-1 signaling.\",\n      \"evidence\": \"RNAi, genetic epistasis, qRT-PCR, and infection assays in C. elegans\",\n      \"pmids\": [\"29719537\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism of p38 suppression not defined\", \"Mammalian relevance of immune role untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Provided structural resolution of the RIOK1\\u2013PRMT5 interaction, mapping a consensus motif binding a novel PRMT5 site distinct from pICln.\",\n      \"evidence\": \"Peptide truncation/mutation studies and protein crystallography of the RioK1 peptide-PRMT5 complex\",\n      \"pmids\": [\"33624332\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of full-length RIOK1 within the complex not determined\", \"How the interface switches with pICln dynamically unresolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established RIOK1 as a direct kinase against G3BP2 at Thr226, linking its catalytic activity to p53 suppression and radioresistance.\",\n      \"evidence\": \"Co-IP, in vitro kinase assay with phosphosite mapping, ubiquitination assays, and in vitro/in vivo functional tests in colorectal cancer\",\n      \"pmids\": [\"35589951\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking G3BP2-T226 to MDM2 activity not fully resolved\", \"Single-lab substrate identification\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Expanded the RIOK1-adapter substrate repertoire by identifying NF90 as a PRMT5 substrate recruited via the RioK1 complex.\",\n      \"evidence\": \"Co-IP, in vitro/in vivo methylation assay, and PRMT5 inhibitor treatment\",\n      \"pmids\": [\"36040368\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of NF90 methylation not defined\", \"Recruitment determinants not mapped\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Positioned RIOK1 as a c-myc/E2F transcriptional target with a ribosome biogenesis function in prostate cancer.\",\n      \"evidence\": \"Transcription factor target analysis, dominant-negative D324A mutant, rRNA quantification, and toyocamycin inhibition\",\n      \"pmids\": [\"37301535\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical role of RIOK1 in rRNA processing not defined\", \"rRNA changes could be indirect via toyocamycin\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined a SPC25-scaffolded RIOK1\\u2013MYH9 trimer in which RIOK1 phosphorylates MYH9-S1943 to drive nuclear MYH9 and Wnt/\\u03b2-catenin-mediated stemness and platinum resistance.\",\n      \"evidence\": \"Co-IP, in vitro kinase assay with phosphosite mutagenesis, nuclear fractionation, inhibitory peptide, and patient-derived organoids\",\n      \"pmids\": [\"39488790\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How SPC25 scaffolding selects MYH9 for phosphorylation not detailed\", \"Link between cytoskeletal disengagement and CTNNB1 transcription mechanistically incomplete\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed a non-catalytic biophysical function: RIOK1 undergoes phase separation to build PTEN-mRNA-sequestering stress granules that reprogram metabolism and confer TKI resistance.\",\n      \"evidence\": \"Phase separation assays, stress granule immunofluorescence, RNA-IP, translation and metabolic profiling, and in vivo TKI resistance models in HCC\",\n      \"pmids\": [\"40467995\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The RIOK1 domain/region driving phase separation not characterized\", \"Selectivity for PTEN mRNA mechanism unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Added YBX1-S165 as a RIOK1 kinase substrate, coupling its catalytic activity to YBX1 nuclear localization and JAK2/STAT3-driven lenvatinib resistance.\",\n      \"evidence\": \"Co-IP, phosphosite identification, nuclear fractionation, functional rescue, and mouse xenograft\",\n      \"pmids\": [\"41354180\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How S165 phosphorylation drives YBX1 nuclear import not defined\", \"Single-lab substrate identification\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how RIOK1's distinct activities — methylosome adapter, ATPase/kinase toward diverse substrates, ribosome biogenesis factor, and phase-separation scaffold — are coordinated or selected within a single cell.\",\n      \"evidence\": \"No integrative study reconciling adapter versus kinase versus condensate functions in the timeline\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified structural/biochemical model linking the functions\", \"Substrate selectivity determinants for the kinase activity undefined\", \"Conditions favoring phase separation versus complex assembly unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [6, 10, 12]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 5, 7]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [10, 12]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [10, 12]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\n      \"PRMT5-WD45/MEP50 methylosome\",\n      \"RIOK1-SPC25-MYH9 trimer\",\n      \"RIOK1-positive stress granules\"\n    ],\n    \"partners\": [\n      \"PRMT5\",\n      \"WD45/MEP50\",\n      \"FBXO6\",\n      \"G3BP2\",\n      \"SPC25\",\n      \"MYH9\",\n      \"YBX1\",\n      \"IGF2BP1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}