{"gene":"EYA1","run_date":"2026-04-28T17:46:03","timeline":{"discoveries":[{"year":1997,"finding":"EYA1 encodes a human homologue of the Drosophila eyes absent gene and defines a novel gene family sharing a highly conserved 271-amino acid C-terminal region (eyaHR/Eya domain); mutations cluster within this domain in BOR syndrome patients.","method":"Positional cloning, sequence analysis, mutation screening","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 1 — foundational cloning paper replicated across multiple subsequent studies","pmids":["9020840"],"is_preprint":false},{"year":1999,"finding":"Eya1 homozygous knockout mice lack ears and kidneys due to defective inductive tissue interactions and apoptotic regression of organ primordia; Six (but not Pax) expression is Eya1-dependent in ear and kidney, placing Eya1 upstream of Six in a conserved Pax-Eya-Six regulatory hierarchy; Gdnf expression in metanephric mesenchyme requires Eya1, positioning Eya1 upstream of Gdnf in the kidney developmental cascade.","method":"Gene knockout (Eya1-/- mice), in situ hybridization, genetic epistasis","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 2 — clean KO with multiple specific molecular readouts, widely replicated","pmids":["10471511"],"is_preprint":false},{"year":2001,"finding":"BOR-associated missense point mutations in the Eya domain do not alter EYA1 protein subcellular localization but disrupt protein-protein interactions (with Six proteins) in both yeast two-hybrid and mammalian cell assays, identifying the Eya domain as the protein-protein interaction interface.","method":"Yeast two-hybrid, co-immunoprecipitation in mammalian cells, immunofluorescence localization","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods in single study with functional mutagenesis","pmids":["11734542"],"is_preprint":false},{"year":2002,"finding":"Eya1 is required for the morphogenesis of thymus, parathyroid, and thyroid; Six1 expression in pharyngeal arch mesenchyme, pouch endoderm, and surface ectoderm is Eya1-dependent, extending the Eya1→Six1 regulatory hierarchy to pharyngeal organogenesis.","method":"Eya1-/- mouse knockout, in situ hybridization, marker gene expression analysis","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined molecular pathway placement","pmids":["12070080"],"is_preprint":false},{"year":2004,"finding":"SIX1 mutations causing BOR/BO syndrome disrupt EYA1-SIX1 protein-protein interaction and SIX1-DNA binding, demonstrating that EYA1 and SIX1 function together as a bipartite transcription complex requiring direct interaction for organogenesis.","method":"Mutation identification by sequencing, protein-protein interaction assays, protein-DNA interaction assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — reciprocal functional assays with disease-causing mutations as mechanistic probes","pmids":["15141091"],"is_preprint":false},{"year":2004,"finding":"Eya1 and Six1 are required for cranial sensory neurogenesis; in the epibranchial placodes, epibranchial progenitor cells fail to express Neurog2 and downstream bHLH and Phox2 genes in Eya1 mutants, placing Eya1 upstream of Neurog2 and neuronal differentiation genes in a conserved Eya-Six regulatory hierarchy.","method":"Eya1-/- and Six1-/- mouse knockouts, in situ hybridization, marker gene expression analysis","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 — clean KO with multiple specific pathway readouts","pmids":["15496442"],"is_preprint":false},{"year":2004,"finding":"Six1 and Eya1 proteins accumulate preferentially in nuclei of fast-twitch muscles; forced coexpression of Six1 and Eya1 in slow-twitch soleus muscle drives fiber-type transition to fast-twitch glycolytic phenotype, identifying Six1/Eya1 as a transcriptional complex controlling skeletal muscle fiber-type identity via MEF3 DNA binding elements.","method":"Immunofluorescence localization, in vivo forced expression in adult muscle, fiber-type marker analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — direct localization with functional overexpression and phenotypic readout","pmids":["15226428"],"is_preprint":false},{"year":2004,"finding":"Eya1HR (Eya domain) interacts with Six1 in yeast two-hybrid assays; Six1 co-expression causes nuclear translocation of cytoplasmic Eya1HR/Eya4HR, demonstrating that Six proteins are required for nuclear localization of Eya proteins.","method":"Yeast two-hybrid, immunofluorescence co-localization","journal":"Journal of the Association for Research in Otolaryngology : JARO","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, replicated concept from prior work but direct localization link confirmed here","pmids":["15492887"],"is_preprint":false},{"year":2006,"finding":"Eya1 and Eya2 act genetically upstream of Pax3 in the formation of ventrolateral dermomyotome hypaxial lips; Six proteins recruit Eya proteins to drive transcription via MEF3 DNA sites during embryogenesis in the somites; double Eya1/Eya2 knockout recapitulates the Six1/Six4 double knockout muscle phenotype, indicating Eya-Six biochemical cooperation is essential for hypaxial myogenesis.","method":"Compound mouse knockouts (Eya1-/-;Eya2-/-, Six1-/-;Six4-/-), genetic epistasis, in vivo transcription reporter assays","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 — multiple compound KO epistasis and transcription assay, moderate replication","pmids":["17098221"],"is_preprint":false},{"year":2008,"finding":"Eya1 co-localizes with Sox2 in inner ear sensory progenitors, and the two proteins physically interact; Eya1 is initially expressed in all sensory region progenitors and later restricted to differentiating hair cells, indicating a concentration-dependent role in regulating sensory organ patterning and hair cell differentiation.","method":"Allelic series (hypomorphic/null), co-immunoprecipitation, immunofluorescence co-localization, marker gene expression","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — allelic series with Co-IP and localization showing functional link","pmids":["18678597"],"is_preprint":false},{"year":2010,"finding":"Sipl1 and Rbck1 are novel Eya1-binding partners identified by GST pulldown and co-immunoprecipitation; these proteins enhance Eya1 co-activator function with Six transcription factors; morpholino knockdown of their zebrafish orthologs produces BOR syndrome-like phenotypes.","method":"GST pulldown, co-immunoprecipitation, morpholino knockdown in zebrafish","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal pulldown/Co-IP plus in vivo functional validation","pmids":["20956555"],"is_preprint":false},{"year":2011,"finding":"Eya1 regulates cell polarity, mitotic spindle orientation, and asymmetric localization of the cell fate determinant Numb in distal embryonic lung epithelium, probably by controlling aPKCζ phosphorylation; loss of Eya1 leads to symmetric Numb segregation and inactivation of Notch signaling, and genetic activation of Notch partially rescues the Eya1-/- lung phenotype.","method":"Eya1-/- mouse knockout, live imaging/immunofluorescence, Notch genetic rescue experiments","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 — KO with defined cellular mechanism and genetic rescue validation","pmids":["21385765"],"is_preprint":false},{"year":2011,"finding":"Murine double mutant of Six1 and Eya1 recapitulates del22q11 (DiGeorge) syndrome features; the Six1/Eya1 transcription complex directly regulates Fgf8 as a downstream effector; Six1/Eya1 genetically interacts with Fgf8 and Tbx1, establishing a Tbx1-Six1/Eya1-Fgf8 genetic pathway controlling cardiovascular and craniofacial morphogenesis.","method":"Compound mouse knockouts, ChIP/direct target validation, genetic interaction analysis","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 — compound KO epistasis with direct target validation, published in high-impact journal","pmids":["21364285"],"is_preprint":false},{"year":2012,"finding":"EYA1 and SIX1 interact directly with SWI/SNF chromatin-remodeling subunits BRG1 and BAF170; the ATPase activity of BRG1 is required for EYA1/SIX1-induced ectopic neurogenesis and normal otocyst neurogenesis; EYA1/SIX1 drive neurogenesis by recruiting the SWI/SNF complex to mediate Neurog1 and NeuroD1 transcription.","method":"Co-immunoprecipitation, gain-of-function overexpression, BRG1 ATPase mutant rescue experiments, in vitro neurogenesis assay","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 — Co-IP plus functional rescue with ATPase mutant, multiple orthogonal approaches","pmids":["22513373"],"is_preprint":false},{"year":2012,"finding":"Eya1/Six1 coexpression in cochlear explants is sufficient to induce hair cell fate in nonsensory epithelium by activating Atoh1-dependent and Atoh1-independent pathways; Sox2 cooperates with Eya1/Six1 to synergistically activate Atoh1 transcription via direct binding to conserved Sox- and Six-binding sites in Atoh1 enhancers; Eya1, Six1, and Sox2 physically interact.","method":"Cochlear explant overexpression, reporter assays with enhancer mutagenesis, co-immunoprecipitation","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 1/2 — reconstitution in explant system, mutagenesis of binding sites, Co-IP","pmids":["22340499"],"is_preprint":false},{"year":2012,"finding":"EYA1 protein level fluctuates during the cell cycle, peaking in mitosis and dropping at M-to-G1 transition; EYA1 is targeted for ubiquitin-mediated proteasomal degradation by APC/C-Cdh1; Cdh1 physically interacts with EYA1, and Cdh1 overexpression reduces EYA1 levels while Cdh1 knockdown stabilizes EYA1.","method":"Co-immunoprecipitation, RNAi knockdown, overexpression, cell cycle synchronization with protein level measurement","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — Co-IP plus gain- and loss-of-function for the E3 ligase adaptor with cell-cycle phenotype","pmids":["23263983"],"is_preprint":false},{"year":2013,"finding":"Crystal structure of SIX1 bound to EYA2 at 2.0 Å reveals SIX1 uses predominantly a single helix to contact EYA; substitution of a single amino acid in this helix disrupts SIX1-EYA interaction, SIX1-mediated EMT, and metastasis in mouse models; structure rationalizes BOR syndrome missense mutations.","method":"X-ray crystallography (2.0 Å), mutagenesis, mouse metastasis model","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 — high-resolution crystal structure with mutagenesis and in vivo functional validation","pmids":["23435380"],"is_preprint":false},{"year":2013,"finding":"EYA1 phosphatase activity is required for breast cancer cell proliferation; EYA1 recruits to the cyclin D1 AP-1 promoter site, and its phosphatase function determines recruitment of CBP, RNA polymerase II, and H3K9 acetylation at that site, driving cyclin D1 transcriptional induction.","method":"Phosphatase domain mutant rescue, chromatin immunoprecipitation (ChIP), reporter assay with AP-1 site mutation","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 1/2 — phosphatase mutant + ChIP with promoter mutagenesis, defines catalytic mechanism","pmids":["23636126"],"is_preprint":false},{"year":2014,"finding":"Eya1 interacts with Six2 and Myc in nephron progenitor cells; Six2 mediates nuclear translocation of Eya1; nuclear Eya1 uses its threonine phosphatase activity to dephosphorylate and stabilize Myc, controlling progenitor cell self-renewal; conditional Eya1 inactivation causes loss of Six2 expression and premature epithelialization.","method":"Conditional knockout, co-immunoprecipitation, cell fate tracing, phosphatase activity assay","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 1/2 — conditional KO, Co-IP, in vitro phosphatase assay, multiple orthogonal approaches","pmids":["25458011"],"is_preprint":false},{"year":2014,"finding":"BOR-associated Eya1 missense mutations S454P, L472R, and L550P lead to enhanced proteasomal degradation of Eya1 protein; Six proteins protect Eya1 from proteasomal degradation, providing a novel disease mechanism; loss of Six interaction (L550P) is sufficient to cause rapid protein degradation.","method":"Proteasome inhibitor assays, co-immunoprecipitation, western blot stability assays","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 — multiple mutants tested with proteasome inhibitor and Co-IP, single lab","pmids":["24489909"],"is_preprint":false},{"year":2014,"finding":"PI3K/Akt1 kinase physically interacts with EYA1, phosphorylates a conserved Akt consensus site on EYA1, and this phosphorylation reduces EYA1 SUMOylation; SUMOylation inhibits EYA1 transcription activity; pharmacologic/genetic PI3K/Akt activation reduces EYA1 SUMOylation and enhances its transcriptional activity.","method":"Co-immunoprecipitation, in vitro kinase assay, SUMOylation assay, transcription reporter assay, mutant rescue in breast cancer cells","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 — Co-IP, in vitro kinase, SUMO assay plus functional rescue with phospho-site mutant","pmids":["24954506"],"is_preprint":false},{"year":2015,"finding":"Eya1 phosphatase activity cooperates with Six1 to promote gene induction in response to Sonic hedgehog (Shh) signaling by regulating Gli transcriptional activators; Eya1 is required for Shh-dependent hindbrain growth and drives medulloblastoma growth.","method":"shRNA phosphatome screen, genetic loss-of-function, reporter assay, in vivo mouse brain tumor model","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 2 — genome-wide screen plus in vivo loss-of-function with defined pathway mechanism","pmids":["25816987"],"is_preprint":false},{"year":2016,"finding":"EYA1's conserved C-terminal haloacid dehalogenase (HAD) domain has dual phosphatase activities (tyrosine and threonine); EYA1 dephosphorylates phospho-T58 of Myc with striking conformational preference; depletion of EYA1 destabilizes Myc by increasing pT58 and promoting FBW7-mediated ubiquitination; both N- and C-terminal domains of EYA1 interact with substrates to enhance catalytic activity.","method":"In vitro phosphatase assay, NMR structural analysis, shRNA depletion, ubiquitination assay, co-immunoprecipitation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — in vitro enzymatic assay + NMR structural evidence + mutagenesis + cell-based validation","pmids":["27795300"],"is_preprint":false},{"year":2017,"finding":"Eya1 threonine phosphatase activity dephosphorylates p-threonine-2122 of the Notch1 intracellular domain (Notch1 ICD), increasing Notch1 ICD stability and maintaining Notch signaling activity in non-neuronal epibranchial placodal cells; this Eya1-Notch axis specifies bipotential epibranchial differentiation into neuronal and non-neuronal lineages.","method":"Eya1-/- mouse knockout, phosphatase activity assays with Notch1 ICD substrate, protein stability assays, genetic lineage tracing","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1/2 — direct phosphatase substrate identification with stability assay and in vivo KO","pmids":["29140246"],"is_preprint":false},{"year":2021,"finding":"Eya1 phosphatase dephosphorylates a critical threonine (T410) in the activation loop of atypical protein kinase C (aPKC), inactivating aPKC; this reduces phosphorylation of Numb and other spindle orientation regulators, promoting Shh-dependent symmetric cell divisions in cerebellar granule cell precursors (GCPs).","method":"In vitro phosphatase assay with aPKC substrate, gain/loss-of-function Shh pathway mutants, spindle orientation imaging, phospho-specific antibodies","journal":"Developmental neuroscience","confidence":"High","confidence_rationale":"Tier 1 — direct enzymatic substrate identification (aPKC T410) with in vivo validation","pmids":["33472197"],"is_preprint":false}],"current_model":"EYA1 is a dual-function protein that acts as both a phosphatase (with tyrosine and threonine phosphatase activities residing in its HAD domain) and a transcriptional co-activator: it physically interacts with SIX family homeodomain proteins (requiring this interaction for nuclear translocation), and together the EYA1-SIX complex recruits SWI/SNF chromatin remodelers and co-activators (CBP, RNA Pol II) to activate target genes (including Neurog1, NeuroD1, Atoh1, Fgf8, cyclin D1) in a conserved PAX-EYA-SIX regulatory hierarchy that is essential for organogenesis of the ear, kidney, thymus, parathyroid, and other organs; EYA1 phosphatase activity directly dephosphorylates aPKC (T410), Notch1 ICD (pT2122), and Myc (pT58) to regulate cell division mode, Notch signaling stability, and Myc protein stability, respectively, while EYA1 protein levels are themselves regulated by APC/C-Cdh1-mediated proteasomal degradation and by PI3K/Akt-dependent reduction of inhibitory SUMOylation."},"narrative":{"teleology":[{"year":1997,"claim":"Positional cloning of EYA1 established it as the first mammalian member of the eyes absent gene family and identified it as the gene mutated in BOR syndrome, with disease mutations clustering in the conserved C-terminal Eya domain.","evidence":"Positional cloning, mutation screening in BOR families","pmids":["9020840"],"confidence":"High","gaps":["Biochemical function of the Eya domain was unknown","No interacting partners identified","No animal model to confirm developmental role"]},{"year":1999,"claim":"Knockout mice revealed that Eya1 is indispensable for ear and kidney organogenesis and placed it upstream of Six genes in a conserved Pax–Eya–Six regulatory hierarchy, establishing the gene's central role in inductive tissue interactions.","evidence":"Eya1-/- knockout mice with in situ hybridization and genetic epistasis","pmids":["10471511"],"confidence":"High","gaps":["Mechanism of Eya1-dependent Six activation unknown (direct transcription vs. protein stabilization)","No biochemical activity assigned to EYA1 protein"]},{"year":2001,"claim":"BOR-associated missense mutations in the Eya domain were shown to disrupt EYA1–SIX protein–protein interaction without altering localization, identifying the Eya domain as the critical interaction interface and providing a molecular explanation for disease pathogenesis.","evidence":"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence with disease-associated mutants","pmids":["11734542"],"confidence":"High","gaps":["Whether the interaction is direct or mediated by bridging factors was unresolved","Structural basis of the interaction unknown"]},{"year":2002,"claim":"The Eya1→Six1 regulatory hierarchy was extended beyond ear and kidney to pharyngeal organ development (thymus, parathyroid, thyroid), establishing EYA1 as a master regulator of multiple organ systems.","evidence":"Eya1-/- knockout mice with in situ hybridization in pharyngeal tissues","pmids":["12070080"],"confidence":"High","gaps":["Direct transcriptional targets in pharyngeal tissues not identified","Whether Eya1 has Six-independent roles in these organs was unclear"]},{"year":2004,"claim":"Multiple studies converged to demonstrate that EYA1 and SIX1 form a bipartite transcriptional complex: SIX1 is required for EYA1 nuclear translocation, EYA1/SIX1 drive neurogenesis via Neurog2, and they control skeletal muscle fiber-type identity via MEF3 elements, while reciprocal SIX1 mutations in BOR confirmed the obligate partnership.","evidence":"SIX1 BOR mutation analysis, Eya1-/- and Six1-/- knockouts, yeast two-hybrid, immunofluorescence, muscle overexpression","pmids":["15141091","15496442","15226428","15492887"],"confidence":"High","gaps":["Whether EYA1 contributes enzymatic activity to the complex or only structural co-activation was unknown","No chromatin-level mechanism for target gene activation"]},{"year":2006,"claim":"Compound Eya1/Eya2 knockout phenocopied the Six1/Six4 double knockout in hypaxial myogenesis, providing genetic proof that Eya proteins are the essential co-factors for Six-dependent transcription during somite development.","evidence":"Compound Eya1-/-;Eya2-/- and Six1-/-;Six4-/- knockouts with in vivo transcription reporters","pmids":["17098221"],"confidence":"High","gaps":["Biochemical mechanism by which Eya potentiates Six transcriptional activity remained undefined"]},{"year":2008,"claim":"EYA1 was found to physically interact with SOX2 and co-localize in sensory progenitors of the inner ear, revealing a Sox2–Eya1 partnership that expanded the known co-activator network beyond SIX proteins.","evidence":"Co-immunoprecipitation, immunofluorescence, Eya1 allelic series in inner ear","pmids":["18678597"],"confidence":"High","gaps":["Functional significance of Sox2–Eya1 interaction for target gene activation not yet tested with enhancer mutagenesis"]},{"year":2011,"claim":"Two studies established that Eya1 controls morphogenesis through distinct mechanisms at different tissue sites: it regulates cell polarity and asymmetric division via aPKC/Numb/Notch in lung epithelium, and the Six1/Eya1 complex directly activates Fgf8 in a Tbx1-dependent pathway controlling cardiovascular and craniofacial development.","evidence":"Eya1-/- knockout with Notch genetic rescue in lung; compound Six1/Eya1 knockouts with ChIP for Fgf8 and genetic interaction with Tbx1","pmids":["21385765","21364285"],"confidence":"High","gaps":["Direct phosphatase substrate in aPKC/Numb pathway not biochemically identified at this point","Whether Eya1 phosphatase activity is required for Fgf8 regulation untested"]},{"year":2012,"claim":"The chromatin-remodeling mechanism of EYA1/SIX1 was defined: they recruit the SWI/SNF complex (BRG1/BAF170) to activate Neurog1 and NeuroD1 transcription, and cooperate with SOX2 to activate Atoh1 via direct binding to conserved enhancer elements, while EYA1 protein levels are themselves regulated by APC/C-Cdh1-mediated proteasomal degradation during the cell cycle.","evidence":"Co-immunoprecipitation of SWI/SNF subunits, BRG1 ATPase-dead rescue, cochlear explant overexpression with enhancer mutagenesis, cell-cycle synchronization with Cdh1 gain/loss-of-function","pmids":["22513373","22340499","23263983"],"confidence":"High","gaps":["Whether SWI/SNF recruitment is direct or bridged by additional factors unclear","Functional consequence of cell-cycle-dependent EYA1 oscillation for developmental decisions not tested"]},{"year":2013,"claim":"A 2.0 Å crystal structure of SIX1 bound to EYA2 revealed the atomic interface and showed that a single-helix contact is essential for EYA interaction, EMT, and metastasis, rationalizing BOR mutations; concurrently, EYA1 phosphatase activity was shown to be required for cyclin D1 transcription via recruitment of CBP and RNA Pol II to the AP-1 promoter site.","evidence":"X-ray crystallography of SIX1–EYA2, mutagenesis, mouse metastasis model; phosphatase-dead mutant rescue with ChIP at cyclin D1 promoter","pmids":["23435380","23636126"],"confidence":"High","gaps":["Structure solved with EYA2, not EYA1; whether interface is identical for EYA1 assumed but not demonstrated crystallographically","How phosphatase activity mechanistically links to CBP recruitment unresolved"]},{"year":2014,"claim":"Multiple studies defined EYA1 regulation and substrate specificity: its threonine phosphatase activity dephosphorylates Myc pT58 to stabilize Myc and maintain nephron progenitor self-renewal; Six proteins protect EYA1 from proteasomal degradation (BOR mutations disrupt this); and PI3K/Akt phosphorylation of EYA1 reduces its inhibitory SUMOylation to enhance transcriptional activity.","evidence":"Conditional kidney KO with Co-IP and phosphatase assay; proteasome inhibitor and stability assays with BOR mutants; in vitro kinase and SUMOylation assays with transcription reporters","pmids":["25458011","24489909","24954506"],"confidence":"High","gaps":["Whether Akt-dependent de-SUMOylation operates in developmental (non-cancer) contexts untested","In vivo validation of PI3K/Akt–EYA1–SUMO axis in organogenesis lacking"]},{"year":2016,"claim":"Biochemical dissection of EYA1's HAD domain established it possesses dual tyrosine and threonine phosphatase activities; NMR analysis revealed striking conformational selectivity for Myc pT58 dephosphorylation, and both N- and C-terminal domains contribute to substrate engagement.","evidence":"In vitro phosphatase assays, NMR structural analysis, shRNA depletion with ubiquitination assays","pmids":["27795300"],"confidence":"High","gaps":["Full substrate spectrum of EYA1 phosphatase undefined","No high-resolution structure of EYA1 HAD domain with bound substrate"]},{"year":2017,"claim":"EYA1 threonine phosphatase was shown to directly dephosphorylate Notch1 ICD at pT2122, stabilizing Notch1 ICD and maintaining Notch signaling in non-neuronal epibranchial placodal cells, providing a mechanistic link between EYA1 phosphatase activity and binary cell fate decisions.","evidence":"Eya1-/- knockout, in vitro phosphatase assay with Notch1 ICD substrate, protein stability and lineage tracing","pmids":["29140246"],"confidence":"High","gaps":["Whether EYA1–Notch axis operates in other Notch-dependent tissues unknown","Kinase responsible for Notch1 T2122 phosphorylation not identified"]},{"year":2021,"claim":"EYA1 was shown to dephosphorylate aPKC at T410 in its activation loop, directly inactivating the kinase and thereby promoting symmetric cell divisions downstream of Shh signaling in cerebellar granule cell precursors, completing the biochemical identification of the aPKC substrate first implicated in 2011.","evidence":"In vitro phosphatase assay with aPKC substrate, Shh pathway gain/loss-of-function, spindle orientation imaging","pmids":["33472197"],"confidence":"High","gaps":["Whether EYA1 dephosphorylates aPKC in lung epithelium (as hypothesized in 2011) not directly tested","Whether other cell polarity substrates exist beyond aPKC unknown"]},{"year":null,"claim":"Key unresolved questions include the full substrate repertoire of EYA1's dual phosphatase activity, whether its phosphatase and co-activator functions are always coupled or independently deployed in different contexts, and the structural basis for EYA1's own HAD domain with substrate bound.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structure of EYA1 HAD domain (structures available are for SIX1–EYA2)","Complete phosphatase substrate catalog undefined","Relative in vivo contributions of phosphatase vs. co-activator functions untested in most organ systems"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[11,17,18,22,23,24]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[6,8,12,13,14,17]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[7,14,18]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[1,3,5,8,9,11,12,14]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[6,13,14,17]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[11,21,23]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[13]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[15]}],"complexes":["EYA1–SIX1 transcriptional complex","EYA1–SIX1–SWI/SNF (BRG1/BAF170)"],"partners":["SIX1","SIX2","SOX2","BRG1","BAF170","CDH1","AKT1"],"other_free_text":[]},"mechanistic_narrative":"EYA1 is a dual-function protein that serves as both a HAD-domain phosphatase and a transcriptional co-activator, operating within a conserved PAX–EYA–SIX regulatory hierarchy essential for organogenesis of the ear, kidney, thymus, parathyroid, and craniofacial structures [PMID:10471511, PMID:12070080, PMID:21364285]. As a co-activator, EYA1 requires physical interaction with SIX-family homeodomain proteins for nuclear translocation and together they recruit SWI/SNF chromatin remodelers (BRG1/BAF170), CBP, and RNA Pol II to activate target genes including Neurog1, NeuroD1, Atoh1, Fgf8, and cyclin D1 [PMID:22513373, PMID:22340499, PMID:23636126]. The EYA1 HAD domain possesses both tyrosine and threonine phosphatase activities and directly dephosphorylates aPKC (T410), Notch1 ICD (pT2122), and Myc (pT58), thereby controlling cell division symmetry, Notch signaling stability, and Myc protein turnover [PMID:33472197, PMID:29140246, PMID:27795300]. Loss-of-function mutations in EYA1 cause branchio-oto-renal (BOR) syndrome, with disease-associated missense mutations disrupting EYA1–SIX interaction and promoting proteasomal degradation of EYA1 [PMID:9020840, PMID:11734542, PMID:24489909]."},"prefetch_data":{"uniprot":{"accession":"Q99502","full_name":"Protein phosphatase EYA1","aliases":["Eyes absent homolog 1"],"length_aa":592,"mass_kda":64.6,"function":"Functions both as protein phosphatase and as transcriptional coactivator for SIX1, and probably also for SIX2, SIX4 and SIX5 (By similarity). Tyrosine phosphatase that dephosphorylates 'Tyr-142' of histone H2AX (H2AXY142ph) and promotes efficient DNA repair via the recruitment of DNA repair complexes containing MDC1. 'Tyr-142' phosphorylation of histone H2AX plays a central role in DNA repair and acts as a mark that distinguishes between apoptotic and repair responses to genotoxic stress (PubMed:19234442). Its function as histone phosphatase may contribute to its function in transcription regulation during organogenesis (By similarity). Also has phosphatase activity with proteins phosphorylated on Ser and Thr residues (in vitro) (By similarity). Required for normal embryonic development of the craniofacial and trunk skeleton, kidneys and ears (By similarity). Together with SIX1, it plays an important role in hypaxial muscle development; in this it is functionally redundant with EYA2 (By similarity)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q99502/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/EYA1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/EYA1","total_profiled":1310},"omim":[{"mim_id":"619019","title":"MICRO RNA 30D; MIR30D","url":"https://www.omim.org/entry/619019"},{"mim_id":"614187","title":"HYPERTELORISM, PREAURICULAR SINUS, PUNCTAL PITS, AND DEAFNESS; HPPD","url":"https://www.omim.org/entry/614187"},{"mim_id":"613705","title":"OROFACIAL CLEFT 10; 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biology","url":"https://pubmed.ncbi.nlm.nih.gov/16154558","citation_count":21,"is_preprint":false},{"pmid":"17364338","id":"PMC_17364338","title":"Phenotypic consequences in a Japanese family having branchio-oto-renal syndrome with a novel frameshift mutation in the gene EYA1.","date":"2007","source":"Acta oto-laryngologica","url":"https://pubmed.ncbi.nlm.nih.gov/17364338","citation_count":21,"is_preprint":false},{"pmid":"8824802","id":"PMC_8824802","title":"Detection of a megabase deletion in a patient with branchio-oto-renal syndrome (BOR) and tricho-rhino-phalangeal syndrome (TRPS): implications for mapping and cloning the BOR gene.","date":"1996","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/8824802","citation_count":21,"is_preprint":false},{"pmid":"31105839","id":"PMC_31105839","title":"EYA1 promotes cell migration and tumor metastasis in hepatocellular carcinoma.","date":"2019","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/31105839","citation_count":20,"is_preprint":false},{"pmid":"30217178","id":"PMC_30217178","title":"Molecular characterization of the genome-wide BOR transporter gene family and genetic analysis of BnaC04.BOR1;1c in Brassica napus.","date":"2018","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/30217178","citation_count":20,"is_preprint":false},{"pmid":"15917575","id":"PMC_15917575","title":"Chromosome-borne class A BOR-1 beta-Lactamase of Bordetella bronchiseptica and Bordetella parapertussis.","date":"2005","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/15917575","citation_count":20,"is_preprint":false},{"pmid":"19206155","id":"PMC_19206155","title":"A recurrent EYA1 mutation causing alternative RNA splicing in branchio-oto-renal syndrome: implications for molecular diagnostics and disease mechanism.","date":"2009","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/19206155","citation_count":20,"is_preprint":false},{"pmid":"15493068","id":"PMC_15493068","title":"EYA1 mutation in a newborn female presenting with cardiofacial syndrome.","date":"2004","source":"Pediatric cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/15493068","citation_count":20,"is_preprint":false},{"pmid":"11558900","id":"PMC_11558900","title":"Genetic features of hearing loss associated with ear anomalies: PDS and EYA1 mutation analysis.","date":"2001","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11558900","citation_count":19,"is_preprint":false},{"pmid":"16790023","id":"PMC_16790023","title":"Characterization of a novel cyclomaltodextrinase expressed from environmental DNA isolated from Bor Khleung hot spring in Thailand.","date":"2006","source":"FEMS microbiology letters","url":"https://pubmed.ncbi.nlm.nih.gov/16790023","citation_count":19,"is_preprint":false},{"pmid":"27012436","id":"PMC_27012436","title":"Biochemical parameters of Spodoptera frugiperda (J. E. Smith) treated with citronella oil (Cymbopogon winterianus Jowitt ex Bor) and its influence on reproduction.","date":"2016","source":"Acta histochemica","url":"https://pubmed.ncbi.nlm.nih.gov/27012436","citation_count":19,"is_preprint":false},{"pmid":"18177466","id":"PMC_18177466","title":"Stickler and branchio-oto-renal syndromes in a patient with mutations in EYA1 and COL2A1 genes.","date":"2007","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18177466","citation_count":18,"is_preprint":false},{"pmid":"24489909","id":"PMC_24489909","title":"BOR-syndrome-associated Eya1 mutations lead to enhanced proteasomal degradation of Eya1 protein.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24489909","citation_count":18,"is_preprint":false},{"pmid":"28947179","id":"PMC_28947179","title":"Six1 and Eya1 both promote and arrest neuronal differentiation by activating multiple Notch pathway genes.","date":"2017","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/28947179","citation_count":18,"is_preprint":false},{"pmid":"23263983","id":"PMC_23263983","title":"The phosphatase-transcription activator EYA1 is targeted by anaphase-promoting complex/Cdh1 for degradation at M-to-G1 transition.","date":"2012","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/23263983","citation_count":17,"is_preprint":false},{"pmid":"28583505","id":"PMC_28583505","title":"Novel EYA1 variants causing Branchio-oto-renal syndrome.","date":"2017","source":"International journal of pediatric otorhinolaryngology","url":"https://pubmed.ncbi.nlm.nih.gov/28583505","citation_count":17,"is_preprint":false},{"pmid":"16005355","id":"PMC_16005355","title":"Identification of a novel mutation in the EYA1 gene in a Korean family with branchio-oto-renal (BOR) syndrome.","date":"2005","source":"International journal of pediatric otorhinolaryngology","url":"https://pubmed.ncbi.nlm.nih.gov/16005355","citation_count":17,"is_preprint":false},{"pmid":"12701758","id":"PMC_12701758","title":"Mutation of the EYA1 gene in patients with branchio-oto syndrome.","date":"2003","source":"Acta oto-laryngologica","url":"https://pubmed.ncbi.nlm.nih.gov/12701758","citation_count":16,"is_preprint":false},{"pmid":"29496520","id":"PMC_29496520","title":"EYA1 promotes tumor angiogenesis by activating the PI3K pathway in colorectal cancer.","date":"2018","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/29496520","citation_count":15,"is_preprint":false},{"pmid":"8092198","id":"PMC_8092198","title":"Localization of branchio-oto-renal (BOR) syndrome to a 3 Mb region of chromosome 8q.","date":"1994","source":"American journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8092198","citation_count":15,"is_preprint":false},{"pmid":"24803398","id":"PMC_24803398","title":"EYA1-related disorders: two clinical cases and a literature review.","date":"2014","source":"International journal of pediatric otorhinolaryngology","url":"https://pubmed.ncbi.nlm.nih.gov/24803398","citation_count":14,"is_preprint":false},{"pmid":"33472197","id":"PMC_33472197","title":"The Eya1 Phosphatase Mediates Shh-Driven Symmetric Cell Division of Cerebellar Granule Cell Precursors.","date":"2021","source":"Developmental neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/33472197","citation_count":14,"is_preprint":false},{"pmid":"35406892","id":"PMC_35406892","title":"Molecular Characterization, Evolutionary Analysis, and Expression Profiling of BOR Genes in Important Cereals.","date":"2022","source":"Plants (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/35406892","citation_count":13,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":44666,"output_tokens":5867,"usd":0.111002},"stage2":{"model":"claude-opus-4-6","input_tokens":9458,"output_tokens":3973,"usd":0.219922},"total_usd":0.330924,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1997,\n      \"finding\": \"EYA1 encodes a human homologue of the Drosophila eyes absent gene and defines a novel gene family sharing a highly conserved 271-amino acid C-terminal region (eyaHR/Eya domain); mutations cluster within this domain in BOR syndrome patients.\",\n      \"method\": \"Positional cloning, sequence analysis, mutation screening\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — foundational cloning paper replicated across multiple subsequent studies\",\n      \"pmids\": [\"9020840\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Eya1 homozygous knockout mice lack ears and kidneys due to defective inductive tissue interactions and apoptotic regression of organ primordia; Six (but not Pax) expression is Eya1-dependent in ear and kidney, placing Eya1 upstream of Six in a conserved Pax-Eya-Six regulatory hierarchy; Gdnf expression in metanephric mesenchyme requires Eya1, positioning Eya1 upstream of Gdnf in the kidney developmental cascade.\",\n      \"method\": \"Gene knockout (Eya1-/- mice), in situ hybridization, genetic epistasis\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with multiple specific molecular readouts, widely replicated\",\n      \"pmids\": [\"10471511\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"BOR-associated missense point mutations in the Eya domain do not alter EYA1 protein subcellular localization but disrupt protein-protein interactions (with Six proteins) in both yeast two-hybrid and mammalian cell assays, identifying the Eya domain as the protein-protein interaction interface.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation in mammalian cells, immunofluorescence localization\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods in single study with functional mutagenesis\",\n      \"pmids\": [\"11734542\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Eya1 is required for the morphogenesis of thymus, parathyroid, and thyroid; Six1 expression in pharyngeal arch mesenchyme, pouch endoderm, and surface ectoderm is Eya1-dependent, extending the Eya1→Six1 regulatory hierarchy to pharyngeal organogenesis.\",\n      \"method\": \"Eya1-/- mouse knockout, in situ hybridization, marker gene expression analysis\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined molecular pathway placement\",\n      \"pmids\": [\"12070080\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"SIX1 mutations causing BOR/BO syndrome disrupt EYA1-SIX1 protein-protein interaction and SIX1-DNA binding, demonstrating that EYA1 and SIX1 function together as a bipartite transcription complex requiring direct interaction for organogenesis.\",\n      \"method\": \"Mutation identification by sequencing, protein-protein interaction assays, protein-DNA interaction assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal functional assays with disease-causing mutations as mechanistic probes\",\n      \"pmids\": [\"15141091\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Eya1 and Six1 are required for cranial sensory neurogenesis; in the epibranchial placodes, epibranchial progenitor cells fail to express Neurog2 and downstream bHLH and Phox2 genes in Eya1 mutants, placing Eya1 upstream of Neurog2 and neuronal differentiation genes in a conserved Eya-Six regulatory hierarchy.\",\n      \"method\": \"Eya1-/- and Six1-/- mouse knockouts, in situ hybridization, marker gene expression analysis\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with multiple specific pathway readouts\",\n      \"pmids\": [\"15496442\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Six1 and Eya1 proteins accumulate preferentially in nuclei of fast-twitch muscles; forced coexpression of Six1 and Eya1 in slow-twitch soleus muscle drives fiber-type transition to fast-twitch glycolytic phenotype, identifying Six1/Eya1 as a transcriptional complex controlling skeletal muscle fiber-type identity via MEF3 DNA binding elements.\",\n      \"method\": \"Immunofluorescence localization, in vivo forced expression in adult muscle, fiber-type marker analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct localization with functional overexpression and phenotypic readout\",\n      \"pmids\": [\"15226428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Eya1HR (Eya domain) interacts with Six1 in yeast two-hybrid assays; Six1 co-expression causes nuclear translocation of cytoplasmic Eya1HR/Eya4HR, demonstrating that Six proteins are required for nuclear localization of Eya proteins.\",\n      \"method\": \"Yeast two-hybrid, immunofluorescence co-localization\",\n      \"journal\": \"Journal of the Association for Research in Otolaryngology : JARO\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, replicated concept from prior work but direct localization link confirmed here\",\n      \"pmids\": [\"15492887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Eya1 and Eya2 act genetically upstream of Pax3 in the formation of ventrolateral dermomyotome hypaxial lips; Six proteins recruit Eya proteins to drive transcription via MEF3 DNA sites during embryogenesis in the somites; double Eya1/Eya2 knockout recapitulates the Six1/Six4 double knockout muscle phenotype, indicating Eya-Six biochemical cooperation is essential for hypaxial myogenesis.\",\n      \"method\": \"Compound mouse knockouts (Eya1-/-;Eya2-/-, Six1-/-;Six4-/-), genetic epistasis, in vivo transcription reporter assays\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple compound KO epistasis and transcription assay, moderate replication\",\n      \"pmids\": [\"17098221\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Eya1 co-localizes with Sox2 in inner ear sensory progenitors, and the two proteins physically interact; Eya1 is initially expressed in all sensory region progenitors and later restricted to differentiating hair cells, indicating a concentration-dependent role in regulating sensory organ patterning and hair cell differentiation.\",\n      \"method\": \"Allelic series (hypomorphic/null), co-immunoprecipitation, immunofluorescence co-localization, marker gene expression\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — allelic series with Co-IP and localization showing functional link\",\n      \"pmids\": [\"18678597\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Sipl1 and Rbck1 are novel Eya1-binding partners identified by GST pulldown and co-immunoprecipitation; these proteins enhance Eya1 co-activator function with Six transcription factors; morpholino knockdown of their zebrafish orthologs produces BOR syndrome-like phenotypes.\",\n      \"method\": \"GST pulldown, co-immunoprecipitation, morpholino knockdown in zebrafish\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal pulldown/Co-IP plus in vivo functional validation\",\n      \"pmids\": [\"20956555\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Eya1 regulates cell polarity, mitotic spindle orientation, and asymmetric localization of the cell fate determinant Numb in distal embryonic lung epithelium, probably by controlling aPKCζ phosphorylation; loss of Eya1 leads to symmetric Numb segregation and inactivation of Notch signaling, and genetic activation of Notch partially rescues the Eya1-/- lung phenotype.\",\n      \"method\": \"Eya1-/- mouse knockout, live imaging/immunofluorescence, Notch genetic rescue experiments\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO with defined cellular mechanism and genetic rescue validation\",\n      \"pmids\": [\"21385765\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Murine double mutant of Six1 and Eya1 recapitulates del22q11 (DiGeorge) syndrome features; the Six1/Eya1 transcription complex directly regulates Fgf8 as a downstream effector; Six1/Eya1 genetically interacts with Fgf8 and Tbx1, establishing a Tbx1-Six1/Eya1-Fgf8 genetic pathway controlling cardiovascular and craniofacial morphogenesis.\",\n      \"method\": \"Compound mouse knockouts, ChIP/direct target validation, genetic interaction analysis\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — compound KO epistasis with direct target validation, published in high-impact journal\",\n      \"pmids\": [\"21364285\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"EYA1 and SIX1 interact directly with SWI/SNF chromatin-remodeling subunits BRG1 and BAF170; the ATPase activity of BRG1 is required for EYA1/SIX1-induced ectopic neurogenesis and normal otocyst neurogenesis; EYA1/SIX1 drive neurogenesis by recruiting the SWI/SNF complex to mediate Neurog1 and NeuroD1 transcription.\",\n      \"method\": \"Co-immunoprecipitation, gain-of-function overexpression, BRG1 ATPase mutant rescue experiments, in vitro neurogenesis assay\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus functional rescue with ATPase mutant, multiple orthogonal approaches\",\n      \"pmids\": [\"22513373\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Eya1/Six1 coexpression in cochlear explants is sufficient to induce hair cell fate in nonsensory epithelium by activating Atoh1-dependent and Atoh1-independent pathways; Sox2 cooperates with Eya1/Six1 to synergistically activate Atoh1 transcription via direct binding to conserved Sox- and Six-binding sites in Atoh1 enhancers; Eya1, Six1, and Sox2 physically interact.\",\n      \"method\": \"Cochlear explant overexpression, reporter assays with enhancer mutagenesis, co-immunoprecipitation\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — reconstitution in explant system, mutagenesis of binding sites, Co-IP\",\n      \"pmids\": [\"22340499\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"EYA1 protein level fluctuates during the cell cycle, peaking in mitosis and dropping at M-to-G1 transition; EYA1 is targeted for ubiquitin-mediated proteasomal degradation by APC/C-Cdh1; Cdh1 physically interacts with EYA1, and Cdh1 overexpression reduces EYA1 levels while Cdh1 knockdown stabilizes EYA1.\",\n      \"method\": \"Co-immunoprecipitation, RNAi knockdown, overexpression, cell cycle synchronization with protein level measurement\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus gain- and loss-of-function for the E3 ligase adaptor with cell-cycle phenotype\",\n      \"pmids\": [\"23263983\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Crystal structure of SIX1 bound to EYA2 at 2.0 Å reveals SIX1 uses predominantly a single helix to contact EYA; substitution of a single amino acid in this helix disrupts SIX1-EYA interaction, SIX1-mediated EMT, and metastasis in mouse models; structure rationalizes BOR syndrome missense mutations.\",\n      \"method\": \"X-ray crystallography (2.0 Å), mutagenesis, mouse metastasis model\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution crystal structure with mutagenesis and in vivo functional validation\",\n      \"pmids\": [\"23435380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"EYA1 phosphatase activity is required for breast cancer cell proliferation; EYA1 recruits to the cyclin D1 AP-1 promoter site, and its phosphatase function determines recruitment of CBP, RNA polymerase II, and H3K9 acetylation at that site, driving cyclin D1 transcriptional induction.\",\n      \"method\": \"Phosphatase domain mutant rescue, chromatin immunoprecipitation (ChIP), reporter assay with AP-1 site mutation\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — phosphatase mutant + ChIP with promoter mutagenesis, defines catalytic mechanism\",\n      \"pmids\": [\"23636126\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Eya1 interacts with Six2 and Myc in nephron progenitor cells; Six2 mediates nuclear translocation of Eya1; nuclear Eya1 uses its threonine phosphatase activity to dephosphorylate and stabilize Myc, controlling progenitor cell self-renewal; conditional Eya1 inactivation causes loss of Six2 expression and premature epithelialization.\",\n      \"method\": \"Conditional knockout, co-immunoprecipitation, cell fate tracing, phosphatase activity assay\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — conditional KO, Co-IP, in vitro phosphatase assay, multiple orthogonal approaches\",\n      \"pmids\": [\"25458011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"BOR-associated Eya1 missense mutations S454P, L472R, and L550P lead to enhanced proteasomal degradation of Eya1 protein; Six proteins protect Eya1 from proteasomal degradation, providing a novel disease mechanism; loss of Six interaction (L550P) is sufficient to cause rapid protein degradation.\",\n      \"method\": \"Proteasome inhibitor assays, co-immunoprecipitation, western blot stability assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple mutants tested with proteasome inhibitor and Co-IP, single lab\",\n      \"pmids\": [\"24489909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PI3K/Akt1 kinase physically interacts with EYA1, phosphorylates a conserved Akt consensus site on EYA1, and this phosphorylation reduces EYA1 SUMOylation; SUMOylation inhibits EYA1 transcription activity; pharmacologic/genetic PI3K/Akt activation reduces EYA1 SUMOylation and enhances its transcriptional activity.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assay, SUMOylation assay, transcription reporter assay, mutant rescue in breast cancer cells\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, in vitro kinase, SUMO assay plus functional rescue with phospho-site mutant\",\n      \"pmids\": [\"24954506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Eya1 phosphatase activity cooperates with Six1 to promote gene induction in response to Sonic hedgehog (Shh) signaling by regulating Gli transcriptional activators; Eya1 is required for Shh-dependent hindbrain growth and drives medulloblastoma growth.\",\n      \"method\": \"shRNA phosphatome screen, genetic loss-of-function, reporter assay, in vivo mouse brain tumor model\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide screen plus in vivo loss-of-function with defined pathway mechanism\",\n      \"pmids\": [\"25816987\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"EYA1's conserved C-terminal haloacid dehalogenase (HAD) domain has dual phosphatase activities (tyrosine and threonine); EYA1 dephosphorylates phospho-T58 of Myc with striking conformational preference; depletion of EYA1 destabilizes Myc by increasing pT58 and promoting FBW7-mediated ubiquitination; both N- and C-terminal domains of EYA1 interact with substrates to enhance catalytic activity.\",\n      \"method\": \"In vitro phosphatase assay, NMR structural analysis, shRNA depletion, ubiquitination assay, co-immunoprecipitation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzymatic assay + NMR structural evidence + mutagenesis + cell-based validation\",\n      \"pmids\": [\"27795300\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Eya1 threonine phosphatase activity dephosphorylates p-threonine-2122 of the Notch1 intracellular domain (Notch1 ICD), increasing Notch1 ICD stability and maintaining Notch signaling activity in non-neuronal epibranchial placodal cells; this Eya1-Notch axis specifies bipotential epibranchial differentiation into neuronal and non-neuronal lineages.\",\n      \"method\": \"Eya1-/- mouse knockout, phosphatase activity assays with Notch1 ICD substrate, protein stability assays, genetic lineage tracing\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — direct phosphatase substrate identification with stability assay and in vivo KO\",\n      \"pmids\": [\"29140246\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Eya1 phosphatase dephosphorylates a critical threonine (T410) in the activation loop of atypical protein kinase C (aPKC), inactivating aPKC; this reduces phosphorylation of Numb and other spindle orientation regulators, promoting Shh-dependent symmetric cell divisions in cerebellar granule cell precursors (GCPs).\",\n      \"method\": \"In vitro phosphatase assay with aPKC substrate, gain/loss-of-function Shh pathway mutants, spindle orientation imaging, phospho-specific antibodies\",\n      \"journal\": \"Developmental neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct enzymatic substrate identification (aPKC T410) with in vivo validation\",\n      \"pmids\": [\"33472197\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EYA1 is a dual-function protein that acts as both a phosphatase (with tyrosine and threonine phosphatase activities residing in its HAD domain) and a transcriptional co-activator: it physically interacts with SIX family homeodomain proteins (requiring this interaction for nuclear translocation), and together the EYA1-SIX complex recruits SWI/SNF chromatin remodelers and co-activators (CBP, RNA Pol II) to activate target genes (including Neurog1, NeuroD1, Atoh1, Fgf8, cyclin D1) in a conserved PAX-EYA-SIX regulatory hierarchy that is essential for organogenesis of the ear, kidney, thymus, parathyroid, and other organs; EYA1 phosphatase activity directly dephosphorylates aPKC (T410), Notch1 ICD (pT2122), and Myc (pT58) to regulate cell division mode, Notch signaling stability, and Myc protein stability, respectively, while EYA1 protein levels are themselves regulated by APC/C-Cdh1-mediated proteasomal degradation and by PI3K/Akt-dependent reduction of inhibitory SUMOylation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"EYA1 is a dual-function protein that serves as both a HAD-domain phosphatase and a transcriptional co-activator, operating within a conserved PAX–EYA–SIX regulatory hierarchy essential for organogenesis of the ear, kidney, thymus, parathyroid, and craniofacial structures [PMID:10471511, PMID:12070080, PMID:21364285]. As a co-activator, EYA1 requires physical interaction with SIX-family homeodomain proteins for nuclear translocation and together they recruit SWI/SNF chromatin remodelers (BRG1/BAF170), CBP, and RNA Pol II to activate target genes including Neurog1, NeuroD1, Atoh1, Fgf8, and cyclin D1 [PMID:22513373, PMID:22340499, PMID:23636126]. The EYA1 HAD domain possesses both tyrosine and threonine phosphatase activities and directly dephosphorylates aPKC (T410), Notch1 ICD (pT2122), and Myc (pT58), thereby controlling cell division symmetry, Notch signaling stability, and Myc protein turnover [PMID:33472197, PMID:29140246, PMID:27795300]. Loss-of-function mutations in EYA1 cause branchio-oto-renal (BOR) syndrome, with disease-associated missense mutations disrupting EYA1–SIX interaction and promoting proteasomal degradation of EYA1 [PMID:9020840, PMID:11734542, PMID:24489909].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Positional cloning of EYA1 established it as the first mammalian member of the eyes absent gene family and identified it as the gene mutated in BOR syndrome, with disease mutations clustering in the conserved C-terminal Eya domain.\",\n      \"evidence\": \"Positional cloning, mutation screening in BOR families\",\n      \"pmids\": [\"9020840\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical function of the Eya domain was unknown\", \"No interacting partners identified\", \"No animal model to confirm developmental role\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Knockout mice revealed that Eya1 is indispensable for ear and kidney organogenesis and placed it upstream of Six genes in a conserved Pax–Eya–Six regulatory hierarchy, establishing the gene's central role in inductive tissue interactions.\",\n      \"evidence\": \"Eya1-/- knockout mice with in situ hybridization and genetic epistasis\",\n      \"pmids\": [\"10471511\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of Eya1-dependent Six activation unknown (direct transcription vs. protein stabilization)\", \"No biochemical activity assigned to EYA1 protein\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"BOR-associated missense mutations in the Eya domain were shown to disrupt EYA1–SIX protein–protein interaction without altering localization, identifying the Eya domain as the critical interaction interface and providing a molecular explanation for disease pathogenesis.\",\n      \"evidence\": \"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence with disease-associated mutants\",\n      \"pmids\": [\"11734542\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the interaction is direct or mediated by bridging factors was unresolved\", \"Structural basis of the interaction unknown\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"The Eya1→Six1 regulatory hierarchy was extended beyond ear and kidney to pharyngeal organ development (thymus, parathyroid, thyroid), establishing EYA1 as a master regulator of multiple organ systems.\",\n      \"evidence\": \"Eya1-/- knockout mice with in situ hybridization in pharyngeal tissues\",\n      \"pmids\": [\"12070080\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct transcriptional targets in pharyngeal tissues not identified\", \"Whether Eya1 has Six-independent roles in these organs was unclear\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Multiple studies converged to demonstrate that EYA1 and SIX1 form a bipartite transcriptional complex: SIX1 is required for EYA1 nuclear translocation, EYA1/SIX1 drive neurogenesis via Neurog2, and they control skeletal muscle fiber-type identity via MEF3 elements, while reciprocal SIX1 mutations in BOR confirmed the obligate partnership.\",\n      \"evidence\": \"SIX1 BOR mutation analysis, Eya1-/- and Six1-/- knockouts, yeast two-hybrid, immunofluorescence, muscle overexpression\",\n      \"pmids\": [\"15141091\", \"15496442\", \"15226428\", \"15492887\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether EYA1 contributes enzymatic activity to the complex or only structural co-activation was unknown\", \"No chromatin-level mechanism for target gene activation\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Compound Eya1/Eya2 knockout phenocopied the Six1/Six4 double knockout in hypaxial myogenesis, providing genetic proof that Eya proteins are the essential co-factors for Six-dependent transcription during somite development.\",\n      \"evidence\": \"Compound Eya1-/-;Eya2-/- and Six1-/-;Six4-/- knockouts with in vivo transcription reporters\",\n      \"pmids\": [\"17098221\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical mechanism by which Eya potentiates Six transcriptional activity remained undefined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"EYA1 was found to physically interact with SOX2 and co-localize in sensory progenitors of the inner ear, revealing a Sox2–Eya1 partnership that expanded the known co-activator network beyond SIX proteins.\",\n      \"evidence\": \"Co-immunoprecipitation, immunofluorescence, Eya1 allelic series in inner ear\",\n      \"pmids\": [\"18678597\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional significance of Sox2–Eya1 interaction for target gene activation not yet tested with enhancer mutagenesis\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Two studies established that Eya1 controls morphogenesis through distinct mechanisms at different tissue sites: it regulates cell polarity and asymmetric division via aPKC/Numb/Notch in lung epithelium, and the Six1/Eya1 complex directly activates Fgf8 in a Tbx1-dependent pathway controlling cardiovascular and craniofacial development.\",\n      \"evidence\": \"Eya1-/- knockout with Notch genetic rescue in lung; compound Six1/Eya1 knockouts with ChIP for Fgf8 and genetic interaction with Tbx1\",\n      \"pmids\": [\"21385765\", \"21364285\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct phosphatase substrate in aPKC/Numb pathway not biochemically identified at this point\", \"Whether Eya1 phosphatase activity is required for Fgf8 regulation untested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"The chromatin-remodeling mechanism of EYA1/SIX1 was defined: they recruit the SWI/SNF complex (BRG1/BAF170) to activate Neurog1 and NeuroD1 transcription, and cooperate with SOX2 to activate Atoh1 via direct binding to conserved enhancer elements, while EYA1 protein levels are themselves regulated by APC/C-Cdh1-mediated proteasomal degradation during the cell cycle.\",\n      \"evidence\": \"Co-immunoprecipitation of SWI/SNF subunits, BRG1 ATPase-dead rescue, cochlear explant overexpression with enhancer mutagenesis, cell-cycle synchronization with Cdh1 gain/loss-of-function\",\n      \"pmids\": [\"22513373\", \"22340499\", \"23263983\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SWI/SNF recruitment is direct or bridged by additional factors unclear\", \"Functional consequence of cell-cycle-dependent EYA1 oscillation for developmental decisions not tested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"A 2.0 Å crystal structure of SIX1 bound to EYA2 revealed the atomic interface and showed that a single-helix contact is essential for EYA interaction, EMT, and metastasis, rationalizing BOR mutations; concurrently, EYA1 phosphatase activity was shown to be required for cyclin D1 transcription via recruitment of CBP and RNA Pol II to the AP-1 promoter site.\",\n      \"evidence\": \"X-ray crystallography of SIX1–EYA2, mutagenesis, mouse metastasis model; phosphatase-dead mutant rescue with ChIP at cyclin D1 promoter\",\n      \"pmids\": [\"23435380\", \"23636126\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure solved with EYA2, not EYA1; whether interface is identical for EYA1 assumed but not demonstrated crystallographically\", \"How phosphatase activity mechanistically links to CBP recruitment unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Multiple studies defined EYA1 regulation and substrate specificity: its threonine phosphatase activity dephosphorylates Myc pT58 to stabilize Myc and maintain nephron progenitor self-renewal; Six proteins protect EYA1 from proteasomal degradation (BOR mutations disrupt this); and PI3K/Akt phosphorylation of EYA1 reduces its inhibitory SUMOylation to enhance transcriptional activity.\",\n      \"evidence\": \"Conditional kidney KO with Co-IP and phosphatase assay; proteasome inhibitor and stability assays with BOR mutants; in vitro kinase and SUMOylation assays with transcription reporters\",\n      \"pmids\": [\"25458011\", \"24489909\", \"24954506\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Akt-dependent de-SUMOylation operates in developmental (non-cancer) contexts untested\", \"In vivo validation of PI3K/Akt–EYA1–SUMO axis in organogenesis lacking\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Biochemical dissection of EYA1's HAD domain established it possesses dual tyrosine and threonine phosphatase activities; NMR analysis revealed striking conformational selectivity for Myc pT58 dephosphorylation, and both N- and C-terminal domains contribute to substrate engagement.\",\n      \"evidence\": \"In vitro phosphatase assays, NMR structural analysis, shRNA depletion with ubiquitination assays\",\n      \"pmids\": [\"27795300\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full substrate spectrum of EYA1 phosphatase undefined\", \"No high-resolution structure of EYA1 HAD domain with bound substrate\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"EYA1 threonine phosphatase was shown to directly dephosphorylate Notch1 ICD at pT2122, stabilizing Notch1 ICD and maintaining Notch signaling in non-neuronal epibranchial placodal cells, providing a mechanistic link between EYA1 phosphatase activity and binary cell fate decisions.\",\n      \"evidence\": \"Eya1-/- knockout, in vitro phosphatase assay with Notch1 ICD substrate, protein stability and lineage tracing\",\n      \"pmids\": [\"29140246\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether EYA1–Notch axis operates in other Notch-dependent tissues unknown\", \"Kinase responsible for Notch1 T2122 phosphorylation not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"EYA1 was shown to dephosphorylate aPKC at T410 in its activation loop, directly inactivating the kinase and thereby promoting symmetric cell divisions downstream of Shh signaling in cerebellar granule cell precursors, completing the biochemical identification of the aPKC substrate first implicated in 2011.\",\n      \"evidence\": \"In vitro phosphatase assay with aPKC substrate, Shh pathway gain/loss-of-function, spindle orientation imaging\",\n      \"pmids\": [\"33472197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether EYA1 dephosphorylates aPKC in lung epithelium (as hypothesized in 2011) not directly tested\", \"Whether other cell polarity substrates exist beyond aPKC unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the full substrate repertoire of EYA1's dual phosphatase activity, whether its phosphatase and co-activator functions are always coupled or independently deployed in different contexts, and the structural basis for EYA1's own HAD domain with substrate bound.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution structure of EYA1 HAD domain (structures available are for SIX1–EYA2)\", \"Complete phosphatase substrate catalog undefined\", \"Relative in vivo contributions of phosphatase vs. co-activator functions untested in most organ systems\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [11, 17, 18, 22, 23, 24]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [6, 8, 12, 13, 14, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [7, 14, 18]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 3, 5, 8, 9, 11, 12, 14]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [6, 13, 14, 17]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [11, 21, 23]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [13]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"complexes\": [\n      \"EYA1–SIX1 transcriptional complex\",\n      \"EYA1–SIX1–SWI/SNF (BRG1/BAF170)\"\n    ],\n    \"partners\": [\n      \"SIX1\",\n      \"SIX2\",\n      \"SOX2\",\n      \"BRG1\",\n      \"BAF170\",\n      \"CDH1\",\n      \"AKT1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}