{"gene":"ANKHD1","run_date":"2026-06-09T22:02:43","timeline":{"discoveries":[{"year":2006,"finding":"ANKHD1 protein is detected in the cytosolic and membrane fractions of cells and co-immunoprecipitates with SHP2 in K562 and LNCaP cell lines, suggesting a scaffolding role in association with SHP2.","method":"Subcellular fractionation and co-immunoprecipitation","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — reciprocal Co-IP not shown, single lab, but replicated in two cell lines","pmids":["16956752"],"is_preprint":false},{"year":2005,"finding":"A splice variant of ANKHD1 lacking the KH domain (VBARP) is primarily localized in the cytoplasm and is essential for cell survival through regulation of caspases, acting in an antiapoptotic capacity.","method":"siRNA knockdown, caspase activity assays, subcellular localization by biochemical fractionation","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — functional siRNA data with caspase readout, single lab, two orthogonal methods","pmids":["16098192"],"is_preprint":false},{"year":2014,"finding":"ANKHD1 binds to SIVA (identified by yeast two-hybrid and confirmed by co-immunoprecipitation), and ANKHD1 silencing leads to Stathmin 1 inactivation and reduced cell migration and proliferation in leukemia cells, likely by inhibiting the SIVA/Stathmin 1 association.","method":"Yeast two-hybrid screen, co-immunoprecipitation, lentiviral shRNA knockdown, cell migration and proliferation assays","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid plus Co-IP plus functional KD, single lab, multiple orthogonal methods","pmids":["25523139"],"is_preprint":false},{"year":2014,"finding":"ANKHD1 is a positive regulator of YAP1 in prostate cancer cells; ANKHD1 silencing downregulates YAP1 expression and activation and reduces CCNA2 (Cyclin A) expression, thereby promoting cell cycle progression.","method":"Lentiviral shRNA knockdown, Western blot, xenograft tumor growth assay","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with defined molecular and cellular phenotype, single lab","pmids":["24726915"],"is_preprint":false},{"year":2012,"finding":"ANKHD1 silencing in multiple myeloma cells delays S-to-G2M cell cycle progression and upregulates the CDK inhibitor p21, irrespective of p53 status.","method":"Lentiviral shRNA knockdown, flow cytometry cell cycle analysis, Western blot","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with defined cell cycle phenotype, single lab, two orthogonal methods","pmids":["23142581"],"is_preprint":false},{"year":2014,"finding":"ANKHD1 interacts with p21 (confirmed by Co-IP and ChIP) and represses the p21 promoter (demonstrated by luciferase reporter assay); ANKHD1 shuttles between cytoplasm and nucleus as shown by nuclear accumulation upon Leptomycin B treatment.","method":"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), luciferase reporter assay, confocal microscopy with Leptomycin B treatment","journal":"European journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, ChIP, luciferase, imaging), single lab","pmids":["25483783"],"is_preprint":false},{"year":2018,"finding":"ANKHD1 physically interacts via its C-terminal KH domain with tumor-suppressing miRNAs (miR-29a, miR-205, miR-196a) as demonstrated by RNA immunoprecipitation, and drives ccRCC cell mitosis primarily by suppressing miR-29a, leading to upregulation of CCND1.","method":"RNA immunoprecipitation (RIP), cell cycle analysis, siRNA knockdown, bioinformatics","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP with functional validation, single lab, multiple orthogonal methods","pmids":["29695508"],"is_preprint":false},{"year":2019,"finding":"ANKHD1 interacts with SMYD3 (identified by mass spectrometry and confirmed functionally); ANKHD1 interacts with H3K4me3 in SMYD3-overexpressing cells and is required for SMYD3-dependent activation of SLUG gene transcription (associated with H3K4me3, H3K9Ac, H3K14Ac marks), promoting HCC migration and invasion.","method":"Mass spectrometry, chromatin immunoprecipitation (ChIP), EMSA, luciferase reporter, siRNA knockdown, migration/invasion assays","journal":"Journal of experimental & clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (MS, ChIP, EMSA, luciferase), single lab","pmids":["30646949"],"is_preprint":false},{"year":2019,"finding":"The ankyrin repeat domain (ARD) of ANKHD1 dimerizes and deforms membranes into tubules and vesicles; specifically, the first 15 ANK repeats form a dimer and the latter 10 ANK repeats enable membrane tubulation/vesiculation via an adjacent amphipathic helix and a positively charged curved structure analogous to BAR domains. ANKHD1 knockdown and localization experiments indicate its involvement in negative regulation of early endosome enlargement.","method":"In vitro membrane deformation assay, dimerization assay, domain mapping, ANKHD1 knockdown with endosome size readout, subcellular localization","journal":"iScience","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of membrane deformation activity, domain mutagenesis/mapping, functional KD with cellular phenotype, multiple orthogonal methods in one study","pmids":["31255983"],"is_preprint":false},{"year":2018,"finding":"ANKHD1 silencing in colorectal cancer cells reduces YAP1 expression and increases YAP1 phosphorylation, inhibits AKT phosphorylation, and suppresses EMT markers (MMP2, MMP9, vimentin, Snail, ZEB1); YAP1 overexpression reverses the effects of ANKHD1 knockdown, placing ANKHD1 upstream of YAP1 in this pathway.","method":"siRNA knockdown, YAP1 overexpression rescue experiment, Western blot, in vivo xenograft","journal":"American journal of cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis via rescue experiment, single lab, multiple readouts","pmids":["30555746"],"is_preprint":false},{"year":2020,"finding":"ANKHD1 interacts with SMYD3 as demonstrated by co-immunoprecipitation and immunofluorescence in NSCLC cells; SMYD3-mediated chemoresistance requires ANKHD1 as co-regulator, and SMYD3 transcriptionally regulates CDK2 promoter (by ChIP) in an ANKHD1-dependent manner.","method":"Co-immunoprecipitation, immunofluorescence, chromatin immunoprecipitation (ChIP), siRNA/overexpression functional assays","journal":"Translational oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus ChIP plus functional rescue, single lab","pmids":["33773404"],"is_preprint":false},{"year":2020,"finding":"ANKHD1 interacts with histone promoter regions (by ChIP) and its silencing downregulates all core histones, implicating ANKHD1 in histone synthesis during S phase; ANKHD1 silencing also reduces PCNA expression and leads to accumulation of γH2AX, indicating a role in DNA repair.","method":"ChIP, Western blot, flow cytometry (γH2AX), siRNA knockdown","journal":"Blood cells, molecules & diseases","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, ChIP plus Western blot but authors note results are preliminary","pmids":["32562952"],"is_preprint":false},{"year":2022,"finding":"ANKHD1 and lncRNA MALAT1 interact (demonstrated by RIP and RNA pulldown); this ANKHD1/MALAT1/YAP1 feedback loop promotes YAP1 transcriptional coactivation and enhances radioresistance in CRC via the YAP1/AKT axis.","method":"RNA immunoprecipitation (RIP), RNA pulldown, siRNA knockdown, in vivo xenograft","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — RIP and RNA pulldown confirm interaction, functional KD, single lab, two orthogonal methods","pmids":["35110552"],"is_preprint":false},{"year":2025,"finding":"ANKHD1 binds to CDK4 and positively controls the Cyclin D1/CDK4 pathway, leading to increased retinoblastoma protein phosphorylation and cell proliferation in a p19-dependent but p21-independent manner; ANKHD1 knockout reduces cystic growth in vitro and in vivo in ADPKD models.","method":"Co-immunoprecipitation (ANKHD1-CDK4 binding), conditional knockout mouse models, Western blot (pRb), in vitro cyst growth assay, in vivo kidney size/function","journal":"Journal of translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus KO with defined molecular and cellular phenotype, single lab, multiple orthogonal methods","pmids":["40457431"],"is_preprint":false},{"year":2025,"finding":"ANKHD1 expression in a TauP301S-PS19 mouse model reduces hyperphosphorylated Tau and is associated with promotion of autophagy as a mechanism to mitigate Tau pathology; ANKHD1 expression restores cognitive performance in affected female PS19 mice.","method":"Transgenic mouse model (Cre-inducible ANKHD1), phospho-Tau immunostaining, behavioral assay (NOR), autophagy markers","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, in vivo gain-of-function with phenotypic readout, autophagy mechanism inferred rather than directly demonstrated","pmids":["40806649"],"is_preprint":false},{"year":2026,"finding":"The acetyltransferase p300 mediates H3K27ac modification at the ANKHD1 promoter to upregulate ANKHD1 expression in response to NNK; ANKHD1 directly interacts with RBM39 to facilitate splicing and expression of MKI67 pre-mRNA, driving CRC cell proliferation and metastasis.","method":"CUT&RUN-seq, mRNA-seq, p300 overexpression/ANKHD1 knockdown functional assays, co-immunoprecipitation (ANKHD1-RBM39), pre-mRNA splicing assay","journal":"Chemico-biological interactions","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CUT&RUN-seq for epigenetic mechanism, Co-IP for protein interaction, functional KD rescue, single lab, multiple orthogonal methods","pmids":["42061695"],"is_preprint":false}],"current_model":"ANKHD1 is a large scaffolding protein with multiple ankyrin repeat domains (mediating protein-protein interactions) and a KH domain (mediating RNA/ssDNA binding) that positively regulates cell proliferation and cycle progression by: (1) acting upstream of YAP1 in the Hippo pathway to promote YAP1 expression and activation; (2) repressing the p21 promoter transcriptionally; (3) binding CDK4 to enhance Cyclin D1/CDK4 activity and retinoblastoma phosphorylation; (4) interacting with SIVA to activate the Stathmin 1 pathway; (5) binding tumor-suppressive miRNAs (miR-29a, miR-205, miR-196a) via its KH domain to suppress them; (6) dimerizing through its ARD to deform endosomal membranes; (7) cooperating with SMYD3 to activate SLUG transcription via histone methylation/acetylation marks; and (8) interacting with RBM39 to regulate pre-mRNA splicing of MKI67, with its expression itself epigenetically controlled by p300-mediated H3K27ac modification."},"narrative":{"mechanistic_narrative":"ANKHD1 is a large multi-domain scaffolding protein that promotes cell proliferation, cell-cycle progression, and tumor cell migration across diverse cancer contexts by coupling protein-protein and RNA-binding activities to growth-control pathways [PMID:24726915, PMID:29695508]. It acts upstream of the Hippo effector YAP1, with silencing reducing YAP1 expression and activation while increasing inhibitory YAP1 phosphorylation, and YAP1 re-expression rescues the loss-of-ANKHD1 phenotype, placing ANKHD1 within a YAP1/AKT signaling axis that controls EMT markers and radioresistance [PMID:24726915, PMID:30555746, PMID:35110552]. ANKHD1 drives the cell cycle through several converging routes: it represses the p21 (CDKN1A) promoter and binds p21 directly while shuttling between cytoplasm and nucleus [PMID:25483783], binds CDK4 to potentiate Cyclin D1/CDK4 activity and retinoblastoma phosphorylation [PMID:40457431], and uses its C-terminal KH domain to bind and suppress tumor-suppressor miRNAs (miR-29a, miR-205, miR-196a), relieving repression of Cyclin D1 [PMID:29695508]. As a chromatin-associated cofactor it partners with the methyltransferase SMYD3 to activate transcription of SLUG and CDK2 in association with active histone marks, promoting migration, invasion, and chemoresistance [PMID:30646949, PMID:33773404], and it interacts with RBM39 to regulate MKI67 pre-mRNA splicing, with its own expression epigenetically induced via p300-mediated H3K27ac [PMID:42061695]. Independently of these growth functions, the ankyrin repeat domain dimerizes and deforms membranes into tubules and vesicles, contributing to negative regulation of early endosome enlargement [PMID:31255983]. Additional reported activities include scaffolding with SHP2, interaction with SIVA to engage the Stathmin 1 pathway, and antiapoptotic regulation of caspases by a KH-domain-deficient splice variant [PMID:16956752, PMID:16098192, PMID:25523139].","teleology":[{"year":2005,"claim":"Established that ANKHD1 (via its KH-domain-lacking splice variant VBARP) has a cell-survival function, the first functional readout for the gene.","evidence":"siRNA knockdown with caspase activity assays and biochemical fractionation","pmids":["16098192"],"confidence":"Medium","gaps":["Mechanism linking ANKHD1 to caspase regulation not defined","Full-length ANKHD1 vs splice variant roles not separated"]},{"year":2006,"claim":"Identified ANKHD1 as a SHP2-associated protein in cytosolic and membrane fractions, framing it as a scaffolding protein.","evidence":"Subcellular fractionation and co-immunoprecipitation in K562 and LNCaP cells","pmids":["16956752"],"confidence":"Medium","gaps":["Reciprocal Co-IP not shown","Functional consequence of the SHP2 association untested"]},{"year":2012,"claim":"Showed ANKHD1 promotes cell-cycle progression by suppressing the CDK inhibitor p21, defining its first cell-cycle mechanism.","evidence":"Lentiviral shRNA knockdown with flow-cytometry cell-cycle analysis and Western blot in multiple myeloma","pmids":["23142581"],"confidence":"Medium","gaps":["Whether p21 regulation is direct not established in this study","Single cell-type context"]},{"year":2014,"claim":"Resolved how ANKHD1 controls p21 — by direct promoter binding and transcriptional repression, with nucleocytoplasmic shuttling enabling nuclear function.","evidence":"Co-IP, ChIP, luciferase reporter, and Leptomycin B imaging","pmids":["25483783"],"confidence":"Medium","gaps":["DNA-binding domain mediating promoter occupancy not mapped","Cofactors at the p21 promoter unknown"]},{"year":2014,"claim":"Connected ANKHD1 to the Hippo effector YAP1 and to the SIVA/Stathmin 1 axis, linking it to proliferation and migration control.","evidence":"Yeast two-hybrid, Co-IP, shRNA knockdown with xenograft and migration/proliferation assays","pmids":["24726915","25523139"],"confidence":"Medium","gaps":["Whether ANKHD1 regulates YAP1 directly or via upstream kinases unresolved","Structural basis of SIVA interaction unknown"]},{"year":2018,"claim":"Defined a direct RNA-binding mechanism: the KH domain binds and suppresses tumor-suppressor miRNAs to derepress Cyclin D1, and placed ANKHD1 upstream of YAP1/AKT-driven EMT.","evidence":"RNA immunoprecipitation, siRNA knockdown with cell-cycle analysis; YAP1 overexpression rescue in colorectal cancer","pmids":["29695508","30555746"],"confidence":"Medium","gaps":["miRNA-binding specificity determinants in the KH domain not mapped","Direct vs indirect control of AKT phosphorylation unclear"]},{"year":2019,"claim":"Revealed a chromatin function — partnering with SMYD3 to activate SLUG via active histone marks — and a structurally distinct membrane-deforming activity of the ankyrin repeat domain.","evidence":"MS, ChIP, EMSA, luciferase for SMYD3/SLUG; in vitro membrane deformation, dimerization, and domain mapping with endosome-size readout","pmids":["30646949","31255983"],"confidence":"High","gaps":["How the same protein partitions between chromatin and membrane roles unknown","Physiological trigger for endosomal regulation undefined"]},{"year":2020,"claim":"Extended the SMYD3 partnership to CDK2 transcriptional control and chemoresistance, and identified an ANKHD1/MALAT1/YAP1 feedback loop governing radioresistance.","evidence":"Co-IP, immunofluorescence, ChIP in NSCLC; RIP and RNA pulldown with knockdown and xenografts in CRC","pmids":["33773404","35110552"],"confidence":"Medium","gaps":["Stoichiometry and assembly order of ANKHD1/SMYD3 and ANKHD1/MALAT1 complexes unknown","Direct lncRNA-binding region not mapped"]},{"year":2020,"claim":"Implicated ANKHD1 in S-phase histone synthesis and DNA repair through histone-promoter occupancy and γH2AX accumulation upon loss.","evidence":"ChIP, Western blot, flow cytometry (γH2AX), siRNA knockdown (authors note preliminary)","pmids":["32562952"],"confidence":"Low","gaps":["Findings noted as preliminary by the authors","Direct vs indirect effect on histone gene transcription unresolved"]},{"year":2025,"claim":"Provided in vivo genetic evidence that ANKHD1 drives proliferation via direct CDK4 binding and Rb phosphorylation, and demonstrated a disease role in ADPKD cystic growth.","evidence":"Co-IP, conditional knockout mouse models, pRb Western blot, in vitro/in vivo cyst growth","pmids":["40457431"],"confidence":"Medium","gaps":["Mechanism of p19-dependence not detailed","Whether CDK4 binding is direct or scaffold-mediated unresolved"]},{"year":2025,"claim":"Reported a protective gain-of-function for ANKHD1 in tauopathy, reducing phospho-Tau and restoring cognition, broadening its biology beyond cancer.","evidence":"Cre-inducible ANKHD1 transgenic PS19 mouse, phospho-Tau immunostaining, behavioral assay, autophagy markers","pmids":["40806649"],"confidence":"Low","gaps":["Autophagy mechanism inferred, not directly demonstrated","Sex-specific effect unexplained"]},{"year":2026,"claim":"Linked carcinogen exposure to ANKHD1 induction via p300/H3K27ac and defined a splicing function through RBM39 to regulate MKI67, tying upstream epigenetic control to a downstream proliferative output.","evidence":"CUT&RUN-seq, mRNA-seq, Co-IP (ANKHD1-RBM39), pre-mRNA splicing assay, knockdown rescue in CRC","pmids":["42061695"],"confidence":"Medium","gaps":["Direct RBM39-ANKHD1 binding interface not mapped","Breadth of ANKHD1-regulated splicing events beyond MKI67 unknown"]},{"year":null,"claim":"How ANKHD1's distinct domains coordinate its membrane-deforming, RNA/miRNA-binding, chromatin, and splicing activities within a single regulatory program remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No integrated structural model of full-length ANKHD1","Unclear which activities are context-specific vs constitutive","Determinants of subcellular partitioning between membrane, cytoplasm, and nucleus undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[6,12]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,5]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[5,7]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[8]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[7]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1,5]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5,7,11]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,9,12]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[4,6,13]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[5,7,10]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[6,15]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[8]}],"complexes":[],"partners":["SHP2","SIVA","YAP1","CDK4","SMYD3","RBM39","MALAT1","CDKN1A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8IWZ3","full_name":"Ankyrin repeat and KH domain-containing protein 1","aliases":["HIV-1 Vpr-binding ankyrin repeat protein","Multiple ankyrin repeats single KH domain","hMASK"],"length_aa":2542,"mass_kda":269.5,"function":"May play a role as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. Isoform 2 may possess an antiapoptotic effect and protect cells during normal cell survival through its regulation of caspases","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q8IWZ3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ANKHD1","classification":"Not Classified","n_dependent_lines":27,"n_total_lines":1208,"dependency_fraction":0.022350993377483443},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ANKRD17","stoichiometry":0.2},{"gene":"DDOST","stoichiometry":0.2},{"gene":"OST4","stoichiometry":0.2},{"gene":"PHAX","stoichiometry":0.2},{"gene":"RPN1","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ANKHD1","total_profiled":1310},"omim":[{"mim_id":"610500","title":"ANKYRIN REPEAT AND KH DOMAIN-CONTAINING PROTEIN 1; ANKHD1","url":"https://www.omim.org/entry/610500"},{"mim_id":"603483","title":"EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 3; EIF4EBP3","url":"https://www.omim.org/entry/603483"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ANKHD1"},"hgnc":{"alias_symbol":["MASK","FLJ20288","FLJ11979","FLJ10042","FLJ14127","KIAA1085","MASK1"],"prev_symbol":[]},"alphafold":{"accession":"Q8IWZ3","domains":[{"cath_id":"1.25.40.20","chopping":"432-531","consensus_level":"medium","plddt":88.9074,"start":432,"end":531},{"cath_id":"1.25.40.20","chopping":"1317-1450","consensus_level":"medium","plddt":88.662,"start":1317,"end":1450},{"cath_id":"3.30.1370.10","chopping":"1696-1777","consensus_level":"medium","plddt":77.0473,"start":1696,"end":1777}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IWZ3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IWZ3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IWZ3-F1-predicted_aligned_error_v6.png","plddt_mean":54.03},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ANKHD1","jax_strain_url":"https://www.jax.org/strain/search?query=ANKHD1"},"sequence":{"accession":"Q8IWZ3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8IWZ3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8IWZ3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IWZ3"}},"corpus_meta":[{"pmid":"24726915","id":"PMC_24726915","title":"ANKHD1, a novel component of the Hippo signaling pathway, promotes YAP1 activation and cell cycle progression in prostate cancer cells.","date":"2014","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/24726915","citation_count":43,"is_preprint":false},{"pmid":"32464549","id":"PMC_32464549","title":"Role of ANKHD1/LINC00346/ZNF655 Feedback Loop in Regulating the Glioma Angiogenesis via Staufen1-Mediated mRNA Decay.","date":"2020","source":"Molecular therapy. Nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/32464549","citation_count":37,"is_preprint":false},{"pmid":"16956752","id":"PMC_16956752","title":"ANKHD1, ankyrin repeat and KH domain containing 1, is overexpressed in acute leukemias and is associated with SHP2 in K562 cells.","date":"2006","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/16956752","citation_count":35,"is_preprint":false},{"pmid":"30646949","id":"PMC_30646949","title":"ANKHD1 is required for SMYD3 to promote tumor metastasis in hepatocellular carcinoma.","date":"2019","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/30646949","citation_count":34,"is_preprint":false},{"pmid":"35110552","id":"PMC_35110552","title":"The feedback loop of ANKHD1/lncRNA MALAT1/YAP1 strengthens the radioresistance of CRC by activating YAP1/AKT signaling.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/35110552","citation_count":32,"is_preprint":false},{"pmid":"23142581","id":"PMC_23142581","title":"ANKHD1 regulates cell cycle progression and proliferation in multiple myeloma cells.","date":"2012","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/23142581","citation_count":29,"is_preprint":false},{"pmid":"25523139","id":"PMC_25523139","title":"ANKHD1 silencing inhibits Stathmin 1 activity, cell proliferation and migration of leukemia cells.","date":"2014","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/25523139","citation_count":26,"is_preprint":false},{"pmid":"29695508","id":"PMC_29695508","title":"Ankyrin repeat and single KH domain 1 (ANKHD1) drives renal cancer cell proliferation via binding to and altering a subset of miRNAs.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29695508","citation_count":25,"is_preprint":false},{"pmid":"25483783","id":"PMC_25483783","title":"ANKHD1 represses p21 (WAF1/CIP1) promoter and promotes multiple myeloma cell growth.","date":"2014","source":"European journal of cancer (Oxford, England : 1990)","url":"https://pubmed.ncbi.nlm.nih.gov/25483783","citation_count":23,"is_preprint":false},{"pmid":"30555746","id":"PMC_30555746","title":"ANKHD1 silencing suppresses the proliferation, migration and invasion of CRC cells by inhibiting YAP1-induced activation of EMT.","date":"2018","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/30555746","citation_count":19,"is_preprint":false},{"pmid":"16098192","id":"PMC_16098192","title":"Molecular and functional characterization of a novel splice variant of ANKHD1 that lacks the KH domain and its role in cell survival and apoptosis.","date":"2005","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/16098192","citation_count":17,"is_preprint":false},{"pmid":"34091845","id":"PMC_34091845","title":"A novel identified circ-ANKHD1 targets the miR-27a-3p/SFRP1 signaling pathway and modulates the apoptosis of granulosa cells.","date":"2021","source":"Environmental science and pollution research international","url":"https://pubmed.ncbi.nlm.nih.gov/34091845","citation_count":15,"is_preprint":false},{"pmid":"31255983","id":"PMC_31255983","title":"Membrane-Deformation Ability of ANKHD1 Is Involved in the Early Endosome Enlargement.","date":"2019","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/31255983","citation_count":15,"is_preprint":false},{"pmid":"32635985","id":"PMC_32635985","title":"Emerging functions for ANKHD1 in cancer-related signaling pathways and cellular processes.","date":"2020","source":"BMB reports","url":"https://pubmed.ncbi.nlm.nih.gov/32635985","citation_count":11,"is_preprint":false},{"pmid":"37629022","id":"PMC_37629022","title":"Evaluating the Molecular Properties and Function of ANKHD1, and Its Role in Cancer.","date":"2023","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37629022","citation_count":9,"is_preprint":false},{"pmid":"33773404","id":"PMC_33773404","title":"SMYD3 confers cisplatin chemoresistance of NSCLC cells in an ANKHD1-dependent manner.","date":"2021","source":"Translational oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33773404","citation_count":9,"is_preprint":false},{"pmid":"36171217","id":"PMC_36171217","title":"Alternative ANKHD1 transcript promotes proliferation and inhibits migration in uterine corpus endometrial carcinoma.","date":"2022","source":"NPJ genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/36171217","citation_count":6,"is_preprint":false},{"pmid":"32562952","id":"PMC_32562952","title":"ANKHD1 is an S phase protein required for histone synthesis and DNA repair in multiple myeloma cells.","date":"2020","source":"Blood cells, molecules & diseases","url":"https://pubmed.ncbi.nlm.nih.gov/32562952","citation_count":5,"is_preprint":false},{"pmid":"35842770","id":"PMC_35842770","title":"ANKHD1 contributes to the malignant phenotype of triple-negative breast cancer cells.","date":"2022","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/35842770","citation_count":3,"is_preprint":false},{"pmid":"40457431","id":"PMC_40457431","title":"ANKHD1 promotes pathogenic proliferation in Autosomal Dominant Polycystic Kidney Disease via the Cyclin D1/CDK4 pathway.","date":"2025","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40457431","citation_count":0,"is_preprint":false},{"pmid":"40806649","id":"PMC_40806649","title":"Upregulating ANKHD1 in PS19 Mice Reduces Tau Phosphorylation and Mitigates Tau Toxicity-Induced Cognitive Deficits.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40806649","citation_count":0,"is_preprint":false},{"pmid":"39605390","id":"PMC_39605390","title":"Upregulating ANKHD1 in PS19 mice reduces Tau phosphorylation and mitigates Tau-toxicity-induced cognitive deficits.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39605390","citation_count":0,"is_preprint":false},{"pmid":"42061695","id":"PMC_42061695","title":"Acetyltransferase p300 promotes NNK-induced colorectal cancer progression by mediating ANKHD1 expression via H3K27ac modification.","date":"2026","source":"Chemico-biological interactions","url":"https://pubmed.ncbi.nlm.nih.gov/42061695","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12883,"output_tokens":3829,"usd":0.048042,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11553,"output_tokens":4201,"usd":0.081395,"stage2_stop_reason":"end_turn"},"total_usd":0.129437,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"ANKHD1 protein is detected in the cytosolic and membrane fractions of cells and co-immunoprecipitates with SHP2 in K562 and LNCaP cell lines, suggesting a scaffolding role in association with SHP2.\",\n      \"method\": \"Subcellular fractionation and co-immunoprecipitation\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — reciprocal Co-IP not shown, single lab, but replicated in two cell lines\",\n      \"pmids\": [\"16956752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"A splice variant of ANKHD1 lacking the KH domain (VBARP) is primarily localized in the cytoplasm and is essential for cell survival through regulation of caspases, acting in an antiapoptotic capacity.\",\n      \"method\": \"siRNA knockdown, caspase activity assays, subcellular localization by biochemical fractionation\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — functional siRNA data with caspase readout, single lab, two orthogonal methods\",\n      \"pmids\": [\"16098192\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ANKHD1 binds to SIVA (identified by yeast two-hybrid and confirmed by co-immunoprecipitation), and ANKHD1 silencing leads to Stathmin 1 inactivation and reduced cell migration and proliferation in leukemia cells, likely by inhibiting the SIVA/Stathmin 1 association.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation, lentiviral shRNA knockdown, cell migration and proliferation assays\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid plus Co-IP plus functional KD, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"25523139\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ANKHD1 is a positive regulator of YAP1 in prostate cancer cells; ANKHD1 silencing downregulates YAP1 expression and activation and reduces CCNA2 (Cyclin A) expression, thereby promoting cell cycle progression.\",\n      \"method\": \"Lentiviral shRNA knockdown, Western blot, xenograft tumor growth assay\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with defined molecular and cellular phenotype, single lab\",\n      \"pmids\": [\"24726915\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"ANKHD1 silencing in multiple myeloma cells delays S-to-G2M cell cycle progression and upregulates the CDK inhibitor p21, irrespective of p53 status.\",\n      \"method\": \"Lentiviral shRNA knockdown, flow cytometry cell cycle analysis, Western blot\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with defined cell cycle phenotype, single lab, two orthogonal methods\",\n      \"pmids\": [\"23142581\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ANKHD1 interacts with p21 (confirmed by Co-IP and ChIP) and represses the p21 promoter (demonstrated by luciferase reporter assay); ANKHD1 shuttles between cytoplasm and nucleus as shown by nuclear accumulation upon Leptomycin B treatment.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), luciferase reporter assay, confocal microscopy with Leptomycin B treatment\",\n      \"journal\": \"European journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, ChIP, luciferase, imaging), single lab\",\n      \"pmids\": [\"25483783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ANKHD1 physically interacts via its C-terminal KH domain with tumor-suppressing miRNAs (miR-29a, miR-205, miR-196a) as demonstrated by RNA immunoprecipitation, and drives ccRCC cell mitosis primarily by suppressing miR-29a, leading to upregulation of CCND1.\",\n      \"method\": \"RNA immunoprecipitation (RIP), cell cycle analysis, siRNA knockdown, bioinformatics\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP with functional validation, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"29695508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ANKHD1 interacts with SMYD3 (identified by mass spectrometry and confirmed functionally); ANKHD1 interacts with H3K4me3 in SMYD3-overexpressing cells and is required for SMYD3-dependent activation of SLUG gene transcription (associated with H3K4me3, H3K9Ac, H3K14Ac marks), promoting HCC migration and invasion.\",\n      \"method\": \"Mass spectrometry, chromatin immunoprecipitation (ChIP), EMSA, luciferase reporter, siRNA knockdown, migration/invasion assays\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (MS, ChIP, EMSA, luciferase), single lab\",\n      \"pmids\": [\"30646949\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The ankyrin repeat domain (ARD) of ANKHD1 dimerizes and deforms membranes into tubules and vesicles; specifically, the first 15 ANK repeats form a dimer and the latter 10 ANK repeats enable membrane tubulation/vesiculation via an adjacent amphipathic helix and a positively charged curved structure analogous to BAR domains. ANKHD1 knockdown and localization experiments indicate its involvement in negative regulation of early endosome enlargement.\",\n      \"method\": \"In vitro membrane deformation assay, dimerization assay, domain mapping, ANKHD1 knockdown with endosome size readout, subcellular localization\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of membrane deformation activity, domain mutagenesis/mapping, functional KD with cellular phenotype, multiple orthogonal methods in one study\",\n      \"pmids\": [\"31255983\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ANKHD1 silencing in colorectal cancer cells reduces YAP1 expression and increases YAP1 phosphorylation, inhibits AKT phosphorylation, and suppresses EMT markers (MMP2, MMP9, vimentin, Snail, ZEB1); YAP1 overexpression reverses the effects of ANKHD1 knockdown, placing ANKHD1 upstream of YAP1 in this pathway.\",\n      \"method\": \"siRNA knockdown, YAP1 overexpression rescue experiment, Western blot, in vivo xenograft\",\n      \"journal\": \"American journal of cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis via rescue experiment, single lab, multiple readouts\",\n      \"pmids\": [\"30555746\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ANKHD1 interacts with SMYD3 as demonstrated by co-immunoprecipitation and immunofluorescence in NSCLC cells; SMYD3-mediated chemoresistance requires ANKHD1 as co-regulator, and SMYD3 transcriptionally regulates CDK2 promoter (by ChIP) in an ANKHD1-dependent manner.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, chromatin immunoprecipitation (ChIP), siRNA/overexpression functional assays\",\n      \"journal\": \"Translational oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus ChIP plus functional rescue, single lab\",\n      \"pmids\": [\"33773404\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ANKHD1 interacts with histone promoter regions (by ChIP) and its silencing downregulates all core histones, implicating ANKHD1 in histone synthesis during S phase; ANKHD1 silencing also reduces PCNA expression and leads to accumulation of γH2AX, indicating a role in DNA repair.\",\n      \"method\": \"ChIP, Western blot, flow cytometry (γH2AX), siRNA knockdown\",\n      \"journal\": \"Blood cells, molecules & diseases\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, ChIP plus Western blot but authors note results are preliminary\",\n      \"pmids\": [\"32562952\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ANKHD1 and lncRNA MALAT1 interact (demonstrated by RIP and RNA pulldown); this ANKHD1/MALAT1/YAP1 feedback loop promotes YAP1 transcriptional coactivation and enhances radioresistance in CRC via the YAP1/AKT axis.\",\n      \"method\": \"RNA immunoprecipitation (RIP), RNA pulldown, siRNA knockdown, in vivo xenograft\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — RIP and RNA pulldown confirm interaction, functional KD, single lab, two orthogonal methods\",\n      \"pmids\": [\"35110552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ANKHD1 binds to CDK4 and positively controls the Cyclin D1/CDK4 pathway, leading to increased retinoblastoma protein phosphorylation and cell proliferation in a p19-dependent but p21-independent manner; ANKHD1 knockout reduces cystic growth in vitro and in vivo in ADPKD models.\",\n      \"method\": \"Co-immunoprecipitation (ANKHD1-CDK4 binding), conditional knockout mouse models, Western blot (pRb), in vitro cyst growth assay, in vivo kidney size/function\",\n      \"journal\": \"Journal of translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus KO with defined molecular and cellular phenotype, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"40457431\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ANKHD1 expression in a TauP301S-PS19 mouse model reduces hyperphosphorylated Tau and is associated with promotion of autophagy as a mechanism to mitigate Tau pathology; ANKHD1 expression restores cognitive performance in affected female PS19 mice.\",\n      \"method\": \"Transgenic mouse model (Cre-inducible ANKHD1), phospho-Tau immunostaining, behavioral assay (NOR), autophagy markers\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, in vivo gain-of-function with phenotypic readout, autophagy mechanism inferred rather than directly demonstrated\",\n      \"pmids\": [\"40806649\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The acetyltransferase p300 mediates H3K27ac modification at the ANKHD1 promoter to upregulate ANKHD1 expression in response to NNK; ANKHD1 directly interacts with RBM39 to facilitate splicing and expression of MKI67 pre-mRNA, driving CRC cell proliferation and metastasis.\",\n      \"method\": \"CUT&RUN-seq, mRNA-seq, p300 overexpression/ANKHD1 knockdown functional assays, co-immunoprecipitation (ANKHD1-RBM39), pre-mRNA splicing assay\",\n      \"journal\": \"Chemico-biological interactions\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CUT&RUN-seq for epigenetic mechanism, Co-IP for protein interaction, functional KD rescue, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"42061695\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ANKHD1 is a large scaffolding protein with multiple ankyrin repeat domains (mediating protein-protein interactions) and a KH domain (mediating RNA/ssDNA binding) that positively regulates cell proliferation and cycle progression by: (1) acting upstream of YAP1 in the Hippo pathway to promote YAP1 expression and activation; (2) repressing the p21 promoter transcriptionally; (3) binding CDK4 to enhance Cyclin D1/CDK4 activity and retinoblastoma phosphorylation; (4) interacting with SIVA to activate the Stathmin 1 pathway; (5) binding tumor-suppressive miRNAs (miR-29a, miR-205, miR-196a) via its KH domain to suppress them; (6) dimerizing through its ARD to deform endosomal membranes; (7) cooperating with SMYD3 to activate SLUG transcription via histone methylation/acetylation marks; and (8) interacting with RBM39 to regulate pre-mRNA splicing of MKI67, with its expression itself epigenetically controlled by p300-mediated H3K27ac modification.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ANKHD1 is a large multi-domain scaffolding protein that promotes cell proliferation, cell-cycle progression, and tumor cell migration across diverse cancer contexts by coupling protein-protein and RNA-binding activities to growth-control pathways [#3, #6]. It acts upstream of the Hippo effector YAP1, with silencing reducing YAP1 expression and activation while increasing inhibitory YAP1 phosphorylation, and YAP1 re-expression rescues the loss-of-ANKHD1 phenotype, placing ANKHD1 within a YAP1/AKT signaling axis that controls EMT markers and radioresistance [#3, #9, #12]. ANKHD1 drives the cell cycle through several converging routes: it represses the p21 (CDKN1A) promoter and binds p21 directly while shuttling between cytoplasm and nucleus [#5], binds CDK4 to potentiate Cyclin D1/CDK4 activity and retinoblastoma phosphorylation [#13], and uses its C-terminal KH domain to bind and suppress tumor-suppressor miRNAs (miR-29a, miR-205, miR-196a), relieving repression of Cyclin D1 [#6]. As a chromatin-associated cofactor it partners with the methyltransferase SMYD3 to activate transcription of SLUG and CDK2 in association with active histone marks, promoting migration, invasion, and chemoresistance [#7, #10], and it interacts with RBM39 to regulate MKI67 pre-mRNA splicing, with its own expression epigenetically induced via p300-mediated H3K27ac [#15]. Independently of these growth functions, the ankyrin repeat domain dimerizes and deforms membranes into tubules and vesicles, contributing to negative regulation of early endosome enlargement [#8]. Additional reported activities include scaffolding with SHP2, interaction with SIVA to engage the Stathmin 1 pathway, and antiapoptotic regulation of caspases by a KH-domain-deficient splice variant [#0, #1, #2].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established that ANKHD1 (via its KH-domain-lacking splice variant VBARP) has a cell-survival function, the first functional readout for the gene.\",\n      \"evidence\": \"siRNA knockdown with caspase activity assays and biochemical fractionation\",\n      \"pmids\": [\"16098192\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking ANKHD1 to caspase regulation not defined\", \"Full-length ANKHD1 vs splice variant roles not separated\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Identified ANKHD1 as a SHP2-associated protein in cytosolic and membrane fractions, framing it as a scaffolding protein.\",\n      \"evidence\": \"Subcellular fractionation and co-immunoprecipitation in K562 and LNCaP cells\",\n      \"pmids\": [\"16956752\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reciprocal Co-IP not shown\", \"Functional consequence of the SHP2 association untested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Showed ANKHD1 promotes cell-cycle progression by suppressing the CDK inhibitor p21, defining its first cell-cycle mechanism.\",\n      \"evidence\": \"Lentiviral shRNA knockdown with flow-cytometry cell-cycle analysis and Western blot in multiple myeloma\",\n      \"pmids\": [\"23142581\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether p21 regulation is direct not established in this study\", \"Single cell-type context\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved how ANKHD1 controls p21 — by direct promoter binding and transcriptional repression, with nucleocytoplasmic shuttling enabling nuclear function.\",\n      \"evidence\": \"Co-IP, ChIP, luciferase reporter, and Leptomycin B imaging\",\n      \"pmids\": [\"25483783\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"DNA-binding domain mediating promoter occupancy not mapped\", \"Cofactors at the p21 promoter unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connected ANKHD1 to the Hippo effector YAP1 and to the SIVA/Stathmin 1 axis, linking it to proliferation and migration control.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, shRNA knockdown with xenograft and migration/proliferation assays\",\n      \"pmids\": [\"24726915\", \"25523139\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ANKHD1 regulates YAP1 directly or via upstream kinases unresolved\", \"Structural basis of SIVA interaction unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined a direct RNA-binding mechanism: the KH domain binds and suppresses tumor-suppressor miRNAs to derepress Cyclin D1, and placed ANKHD1 upstream of YAP1/AKT-driven EMT.\",\n      \"evidence\": \"RNA immunoprecipitation, siRNA knockdown with cell-cycle analysis; YAP1 overexpression rescue in colorectal cancer\",\n      \"pmids\": [\"29695508\", \"30555746\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"miRNA-binding specificity determinants in the KH domain not mapped\", \"Direct vs indirect control of AKT phosphorylation unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed a chromatin function — partnering with SMYD3 to activate SLUG via active histone marks — and a structurally distinct membrane-deforming activity of the ankyrin repeat domain.\",\n      \"evidence\": \"MS, ChIP, EMSA, luciferase for SMYD3/SLUG; in vitro membrane deformation, dimerization, and domain mapping with endosome-size readout\",\n      \"pmids\": [\"30646949\", \"31255983\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the same protein partitions between chromatin and membrane roles unknown\", \"Physiological trigger for endosomal regulation undefined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended the SMYD3 partnership to CDK2 transcriptional control and chemoresistance, and identified an ANKHD1/MALAT1/YAP1 feedback loop governing radioresistance.\",\n      \"evidence\": \"Co-IP, immunofluorescence, ChIP in NSCLC; RIP and RNA pulldown with knockdown and xenografts in CRC\",\n      \"pmids\": [\"33773404\", \"35110552\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Stoichiometry and assembly order of ANKHD1/SMYD3 and ANKHD1/MALAT1 complexes unknown\", \"Direct lncRNA-binding region not mapped\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Implicated ANKHD1 in S-phase histone synthesis and DNA repair through histone-promoter occupancy and γH2AX accumulation upon loss.\",\n      \"evidence\": \"ChIP, Western blot, flow cytometry (γH2AX), siRNA knockdown (authors note preliminary)\",\n      \"pmids\": [\"32562952\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Findings noted as preliminary by the authors\", \"Direct vs indirect effect on histone gene transcription unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Provided in vivo genetic evidence that ANKHD1 drives proliferation via direct CDK4 binding and Rb phosphorylation, and demonstrated a disease role in ADPKD cystic growth.\",\n      \"evidence\": \"Co-IP, conditional knockout mouse models, pRb Western blot, in vitro/in vivo cyst growth\",\n      \"pmids\": [\"40457431\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of p19-dependence not detailed\", \"Whether CDK4 binding is direct or scaffold-mediated unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Reported a protective gain-of-function for ANKHD1 in tauopathy, reducing phospho-Tau and restoring cognition, broadening its biology beyond cancer.\",\n      \"evidence\": \"Cre-inducible ANKHD1 transgenic PS19 mouse, phospho-Tau immunostaining, behavioral assay, autophagy markers\",\n      \"pmids\": [\"40806649\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Autophagy mechanism inferred, not directly demonstrated\", \"Sex-specific effect unexplained\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Linked carcinogen exposure to ANKHD1 induction via p300/H3K27ac and defined a splicing function through RBM39 to regulate MKI67, tying upstream epigenetic control to a downstream proliferative output.\",\n      \"evidence\": \"CUT&RUN-seq, mRNA-seq, Co-IP (ANKHD1-RBM39), pre-mRNA splicing assay, knockdown rescue in CRC\",\n      \"pmids\": [\"42061695\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct RBM39-ANKHD1 binding interface not mapped\", \"Breadth of ANKHD1-regulated splicing events beyond MKI67 unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ANKHD1's distinct domains coordinate its membrane-deforming, RNA/miRNA-binding, chromatin, and splicing activities within a single regulatory program remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No integrated structural model of full-length ANKHD1\", \"Unclear which activities are context-specific vs constitutive\", \"Determinants of subcellular partitioning between membrane, cytoplasm, and nucleus undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [6, 12]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 5]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [5, 7]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1, 5]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5, 7, 11]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 9, 12]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [4, 6, 13]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [5, 7, 10]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [6, 15]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"SHP2\", \"SIVA\", \"YAP1\", \"CDK4\", \"SMYD3\", \"RBM39\", \"MALAT1\", \"CDKN1A\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}