{"gene":"SPDYA","run_date":"2026-06-10T07:46:39","timeline":{"discoveries":[{"year":2003,"finding":"Spy1 directly interacts with the CDK inhibitor p27Kip1 (confirmed by yeast two-hybrid, in vitro pulldown with bacterially expressed proteins, and co-immunoprecipitation of endogenous and transfected proteins in mammalian cells), and this interaction allows Spy1 to overcome p27-induced G1 arrest to promote CDK2-dependent DNA synthesis; proliferative effects of Spy1 require endogenous p27.","method":"Yeast two-hybrid screen, in vitro pulldown (bacterially expressed proteins), co-immunoprecipitation, CDK2 histone H1 kinase assay, p27-null cell rescue experiments","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (Y2H, in vitro pulldown, co-IP, kinase assay, genetic rescue) in one study, subsequently replicated by other labs","pmids":["12972555"],"is_preprint":false},{"year":2003,"finding":"Human Spy1 binds and activates CDK2 during the DNA damage response; Spy1 overexpression enhances cell viability after genotoxic damage (camptothecin, cisplatin, hydroxyurea), and a dominant-negative CDK2 overrides Spy1 function, demonstrating that CDK2 activation is required for Spy1-mediated cell survival.","method":"Clonogenic survival assays, comet assays, dominant-negative CDK2 expression, siRNA knockdown, endogenous protein level analysis by western blot","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — dominant-negative epistasis and siRNA knockdown with multiple damage readouts, single lab","pmids":["12839962"],"is_preprint":false},{"year":2006,"finding":"Spy1 expression suppresses UV-induced caspase-3 activation and apoptosis, allows UV-irradiation-resistant DNA synthesis and mitotic entry (histone H3 phosphorylation), and inhibits phosphorylation of Chk1, RPA, and histone H2A.X; mutation of the conserved Speedy/Ringo box (CDK2-interaction domain) abrogates these effects, placing CDK2 activation upstream of checkpoint bypass and apoptosis suppression.","method":"Inducible Spy1 expression system, flow cytometry, western blot for checkpoint markers, Speedy/Ringo box point mutant","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — inducible system with mutagenesis and multiple orthogonal readouts, single lab","pmids":["16951407"],"is_preprint":false},{"year":2007,"finding":"Spy1 activates CDK2 to phosphorylate p27Kip1 at T187 in vitro using recombinant proteins; Spy1/CDK2 added to a preformed inhibited cyclin E/CDK2/p27 complex promotes T187 phosphorylation; in cells, inducible Spy1 expression reduces endogenous p27 and exogenous p27WT but not p27T187A, and synchronised cells show enhanced T187 phosphorylation and p27 degradation in late G1 and S-phase.","method":"In vitro kinase assay with recombinant proteins, inducible expression system, synchronized HeLa cell analysis, T187A mutant control, western blot","journal":"Cell cycle","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstituted in vitro kinase assay plus cell-based mutagenesis validation, single lab but multiple orthogonal methods","pmids":["17671428"],"is_preprint":false},{"year":2009,"finding":"Spy1-mediated inhibition of apoptosis and bypass of UV-induced checkpoint activation requires the presence of functional p53 and the CDK inhibitor p21; Spy1 expression prevents nucleotide excision repair of cyclobutane pyrimidine dimers, increases cellular mutation frequency, reduces cyclin E-induced γH2A.X foci formation, and knockdown of endogenous Spy1 itself leads to γH2A.X foci, Chk1 phosphorylation, and proliferation defects.","method":"siRNA knockdown, p53/p21 genetic requirement analysis, CPD repair assay, mutation frequency assay, γH2A.X and Chk1 phosphorylation western blot","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis with p53/p21, endogenous knockdown with multiple readouts, single lab","pmids":["19106603"],"is_preprint":false},{"year":2012,"finding":"Spy1 facilitates mammary cell transformation in a manner dependent on activation of CDK1, with subsequent inhibition of the anti-apoptotic regulator FOXO1; knockdown of Spy1 impairs breast cancer cell proliferation.","method":"CDK1 activity assays, FOXO1 functional analysis, shRNA knockdown, in vivo mouse mammary tumor model","journal":"BMC cancer","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — CDK1 and FOXO1 mechanistic follow-up with in vivo support, single lab","pmids":["22280365"],"is_preprint":false},{"year":2015,"finding":"Spy1 directly binds SCG10 (a microtubule-destabilising protein/axonal maintenance factor) and mediates SCG10 phosphorylation and proteasomal degradation in a partially JNK-dependent manner following sciatic nerve injury; inhibition of Spy1 attenuates SCG10 phosphorylation and delays axonal degeneration.","method":"Co-immunoprecipitation, in vitro binding assay, western blot for phosphorylation/degradation, Spy1 inhibition with phenotypic rescue","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — co-IP plus functional inhibition with defined pathway placement, single lab","pmids":["25869138"],"is_preprint":false},{"year":2015,"finding":"Spy1 interacts with CLIPR-59 in glioblastoma cells, sequestering CLIPR-59 away from CYLD (a K63-deubiquitinase); knockdown of Spy1 increases CLIPR-59-CYLD association, enhances K63-deubiquitination of RIP1, and promotes caspase-8/caspase-3 activation, thereby sensitising GBM cells to TNF-α-induced apoptosis.","method":"Co-immunoprecipitation, siRNA knockdown, ubiquitination assay, caspase activity assays, western blot","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — co-IP plus mechanistic epistasis, single lab","pmids":["26017671"],"is_preprint":false},{"year":2016,"finding":"Specific residues in Spy1 mediate direct interaction with CDK2 and separately with p27Kip1; point mutations disrupting each interaction reduce endogenous CDK2 activity and Spy1-mediated proliferation; only the p27-interaction mutation abolishes Spy1-mediated p27 destabilisation, while disruption of either interaction slows Spy1-driven tumorigenesis in vivo.","method":"Site-directed mutagenesis, co-immunoprecipitation, CDK2 kinase assay, p27 stability assay, in vivo mouse tumour model","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — mutagenesis with biochemical and in vivo validation, single lab","pmids":["26771716"],"is_preprint":false},{"year":2017,"finding":"Crystal structures of the Cdk2-Spy1 binary complex and the p27-Cdk2-Spy1 ternary complex reveal that Spy1 activates Cdk2 by inducing structural changes that bypass the requirement for activation-loop phosphorylation; Spy1 lacks the cyclin-binding groove that mediates p27 inhibition and substrate cyclin-docking, explaining why Cdk-Spy1 complexes are resistant to p27 and have altered substrate specificity; Spy1 mutations that ablate Cdk2 binding also abolish cell proliferation.","method":"X-ray crystallography, in vitro CDK2 kinase assay, site-directed mutagenesis, cell proliferation assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures of two complexes with mutagenesis and functional validation, single rigorous study with multiple orthogonal methods","pmids":["28666995"],"is_preprint":false},{"year":2017,"finding":"Spy1 activates ERK1/2 in a MEK-independent manner; Spy1-mediated ERK activation increases ligand-independent phosphorylation and activation of estrogen receptor α, correlating with decreased tamoxifen sensitivity in breast cancer cells.","method":"ERK1/2 phosphorylation assays, MEK inhibitor controls, ERα phosphorylation assays, tamoxifen sensitivity assays, Spy1 overexpression/knockdown","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — pharmacological epistasis with MEK inhibitor and ERα phosphorylation readout, single lab","pmids":["28423577"],"is_preprint":false},{"year":2019,"finding":"p53 controls Spy1 protein levels via proteasomal degradation mediated in part by the E3 ubiquitin ligase Nedd4; loss or mutation of p53 allows Spy1 accumulation, leading to mammary hyperplasia; in a transgenic mouse model, sustained Spy1 elevation results in increased mammary proliferation and tumour susceptibility.","method":"Transgenic mouse model, in vitro protein stability assays, Nedd4 co-immunoprecipitation/ubiquitination, p53 knockout/mutation analysis","journal":"Breast cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Nedd4-mediated ubiquitination supported by co-IP and in vivo transgenic model, single lab","pmids":["31829284"],"is_preprint":false},{"year":2020,"finding":"SPDYA (Speedy A) directly interacts with SUN1 at the nuclear envelope via its Ringo domain and recruits CDK2 to SUN1; the SPDYA-binding site on SUN1 is in the N-terminal domain, close to the MAJIN-binding site; CDK2 inhibitors decrease the SUN1-MAJIN interaction, suggesting SPDYA-CDK2 promotes telomere-nuclear envelope attachment during meiosis.","method":"Co-immunoprecipitation, domain-mapping experiments, CDK2 inhibitor treatment, binding-site mutagenesis","journal":"Frontiers in cell and developmental biology","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — co-IP and domain mapping with pharmacological epistasis, single lab","pmids":["33015044"],"is_preprint":false},{"year":2021,"finding":"SPDYA directly interacts with SUN1; the crystal structure of the human SUN1-SPDYA-CDK2 ternary complex was determined; SUN1 mutations that disrupt SPDYA binding in mice impair telomere-LINC complex attachment, abolish the ring-shaped telomere supramolecular architecture at the nuclear envelope, and cause defects in homologous pairing and synapsis during meiosis prophase I.","method":"X-ray crystallography (ternary complex), site-directed mutagenesis of SUN1, mouse genetic model (SPDYA-binding-deficient SUN1 knockin), meiosis phenotype analysis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure of ternary complex combined with in vivo mouse genetic validation, multiple orthogonal methods in single rigorous study","pmids":["34039995"],"is_preprint":false},{"year":2021,"finding":"SPY1 activates the epigenetic regulator EZH2 to promote H3K27me3-mediated repression of CDK inhibitors CDKN1A and CDKN2A, overriding senescence during reprogramming; SPY1 is required for efficient reprogramming of mouse fibroblasts to induced pluripotent stem cells.","method":"iPSC reprogramming assay, EZH2 activity/H3K27me3 western blot, Spy1 knockdown/overexpression, CDKN1A/CDKN2A expression analysis","journal":"Stem cells","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — functional reprogramming assay with epigenetic readout, single lab","pmids":["34486784"],"is_preprint":false},{"year":2022,"finding":"SPY1 protein is degraded via ubiquitination mediated by MDM2 (an E3 ubiquitin ligase) in ALS motor neurons; overexpression of Spy1 suppresses ferroptosis in hSOD1G93A cells by restoring the GCH1/BH4 axis (a ferroptosis resistance pathway) and reducing TFR1-mediated iron import, decreasing lipid peroxidation; neuron-specific Spy1 overexpression delays disease onset and extends survival in ALS transgenic mice.","method":"Ubiquitination assay, MDM2 knockdown/overexpression, lipid peroxidation measurement, GCH1/TFR1 western blot and activity assays, transgenic mouse model with neurological scoring","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination assay plus in vivo mouse model with mechanistic pathway analysis, single lab","pmids":["36443440"],"is_preprint":false},{"year":2022,"finding":"Spy1 stabilises c-Myc protein in TNBC cells; knockdown of Spy1 reduces c-Myc protein levels and sensitises TNBC cells to chemotherapy; Spy1 protein levels positively correlate with c-Myc protein (not mRNA) levels in TNBC patient samples.","method":"shRNA knockdown, western blot for c-Myc protein, chemotherapy sensitivity assays, tissue microarray","journal":"Breast cancer research and treatment","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-regulation observed by knockdown and protein correlation, mechanism of stabilisation not biochemically defined, single lab","pmids":["36029387"],"is_preprint":false},{"year":2023,"finding":"RingoA (Spy1 ortholog in mouse) regulates exit from quiescence in adult neural stem cells; RingoA expression increases CDK activity and facilitates cell cycle entry; RingoA-deficient mice show reduced olfactory neurogenesis and accumulation of quiescent NSCs, placing RingoA as a CDK activity threshold regulator for NSC quiescence-to-activation transition.","method":"RingoA knockout mouse, CDK activity assays, neurogenesis quantification, quiescent NSC accumulation analysis","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO mouse with CDK activity and neurogenesis phenotypes, single lab","pmids":["36876138"],"is_preprint":false},{"year":2014,"finding":"CRMP1 interacts with Spy1 (identified by yeast two-hybrid and confirmed by co-IP); Spy1 affects CDK5-mediated CRMP1 phosphorylation, which disrupts CRMP1-actin association and contributes to Sema3A-induced growth cone collapse and impaired regeneration after sciatic nerve crush.","method":"Yeast two-hybrid, co-immunoprecipitation, overexpression/shRNA, CRMP1 phosphorylation assay, growth cone collapse assay, rat sciatic nerve crush model","journal":"Molecular neurobiology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, co-IP plus limited mechanistic follow-up of CDK5-CRMP1 phosphorylation axis","pmids":["25526860"],"is_preprint":false}],"current_model":"SPDYA (Spy1) is an atypical 'cyclin-like' CDK activator that binds and activates CDK2 (and CDK1) through a structurally distinct mechanism—confirmed by crystal structures of the CDK2-Spy1 and p27-CDK2-Spy1 complexes—that confers activation-loop-phosphorylation independence and resistance to p27 inhibition; Spy1 promotes G1/S progression by directly binding p27Kip1 and stimulating CDK2-mediated p27-T187 phosphorylation and degradation, bypasses DNA-damage checkpoints and apoptosis through CDK2 in a p53/p21-dependent context, is itself degraded by the MDM2 and Nedd4 E3 ubiquitin ligases, activates ERK1/2 in a MEK-independent manner to drive ERα signalling, stabilises c-Myc, activates EZH2-mediated H3K27me3 to silence CDK inhibitors during reprogramming, interacts with SUN1 at the nuclear envelope via its Ringo domain to recruit CDK2 and support telomere attachment during meiosis prophase I, and regulates neural stem cell quiescence exit as well as axonal degeneration through SCG10 phosphorylation."},"narrative":{"mechanistic_narrative":"SPDYA (Spy1/RingoA) is an atypical, cyclin-like activator of cyclin-dependent kinases that drives cell-cycle entry and proliferation through a structurally distinct mechanism of CDK2/CDK1 activation [PMID:12972555, PMID:28666995]. Crystal structures of the CDK2-Spy1 binary and p27-CDK2-Spy1 ternary complexes show that Spy1 induces conformational changes that activate CDK2 independently of activation-loop phosphorylation, and that Spy1 lacks the cyclin-binding groove, rendering Spy1-CDK2 complexes resistant to p27 inhibition and altering substrate specificity [PMID:28666995]. Spy1 directly binds the CDK inhibitor p27Kip1 through residues separable from its CDK2-interaction surface, and stimulates CDK2-mediated phosphorylation of p27 at T187, triggering its degradation to overcome p27-induced G1 arrest and promote S-phase entry [PMID:12972555, PMID:17671428, PMID:26771716]. Through CDK2 activation Spy1 suppresses DNA-damage checkpoints and apoptosis in a p53/p21-dependent context, permitting damage-resistant DNA synthesis and mitotic entry while impairing repair fidelity [PMID:12839962, PMID:16951407, PMID:19106603]. Spy1 promotes mammary transformation via CDK1 activation and FOXO1 inhibition, activates ERK1/2 in a MEK-independent manner to drive ligand-independent ERα signalling and tamoxifen resistance, and engages epigenetic silencing of CDK inhibitors via EZH2/H3K27me3 to override senescence during reprogramming [PMID:22280365, PMID:28423577, PMID:34486784]. Spy1 protein abundance is controlled by proteasomal degradation through the E3 ligases Nedd4 (downstream of p53) and MDM2 [PMID:31829284, PMID:36443440]. Beyond cell-cycle control, Spy1 uses its Ringo domain to bind SUN1 at the nuclear envelope and recruit CDK2 to support telomere-LINC complex attachment, homologous pairing and synapsis during meiosis prophase I [PMID:33015044, PMID:34039995], and regulates neural stem-cell exit from quiescence as a CDK activity threshold setter [PMID:36876138].","teleology":[{"year":2003,"claim":"Established that Spy1 physically binds the CDK inhibitor p27Kip1 and uses this interaction to bypass p27-imposed G1 arrest, defining a mechanism by which Spy1 overrides a key proliferation brake.","evidence":"Yeast two-hybrid, in vitro pulldown, co-IP, CDK2 H1 kinase assay, and p27-null rescue in mammalian cells","pmids":["12972555"],"confidence":"High","gaps":["Did not resolve whether Spy1 phosphorylates p27 directly or via CDK2","Structural basis of p27 binding unresolved"]},{"year":2003,"claim":"Showed Spy1 binds and activates CDK2 to promote survival after genotoxic damage, with dominant-negative CDK2 abolishing the effect, placing CDK2 activation as the required effector of Spy1-mediated cell survival.","evidence":"Clonogenic and comet assays, dominant-negative CDK2, siRNA knockdown across multiple damaging agents","pmids":["12839962"],"confidence":"Medium","gaps":["Single lab","Did not define which checkpoint nodes are bypassed"]},{"year":2006,"claim":"Demonstrated that Spy1 suppresses UV-induced apoptosis and checkpoint signalling (Chk1, RPA, H2A.X) in a manner dependent on the Speedy/Ringo box, placing CDK2 activation upstream of checkpoint bypass.","evidence":"Inducible Spy1 expression, flow cytometry, checkpoint-marker westerns, Ringo-box point mutant","pmids":["16951407"],"confidence":"Medium","gaps":["Mechanism of checkpoint suppression not biochemically dissected","Single lab"]},{"year":2007,"claim":"Reconstituted the biochemical core of Spy1 function by showing Spy1/CDK2 phosphorylates p27 at T187 in vitro and drives T187-dependent p27 degradation in cells, linking Spy1 directly to controlled p27 turnover.","evidence":"In vitro kinase assay with recombinant proteins, inducible expression, synchronized HeLa cells, T187A mutant control","pmids":["17671428"],"confidence":"High","gaps":["Did not identify the ubiquitin ligase acting on phospho-T187 p27 in this context"]},{"year":2009,"claim":"Defined the genetic context of checkpoint bypass, showing Spy1's anti-apoptotic and checkpoint-overriding effects require functional p53 and p21 and come at the cost of impaired excision repair and increased mutation frequency.","evidence":"siRNA knockdown, p53/p21 requirement analysis, CPD repair and mutation-frequency assays, γH2A.X/Chk1 westerns","pmids":["19106603"],"confidence":"Medium","gaps":["Mechanistic basis of repair inhibition unresolved","Single lab"]},{"year":2012,"claim":"Extended Spy1's transforming role to CDK1, showing mammary transformation depends on CDK1 activation and FOXO1 inhibition, broadening Spy1's CDK targets beyond CDK2.","evidence":"CDK1 activity assays, FOXO1 analysis, shRNA, in vivo mouse mammary tumor model","pmids":["22280365"],"confidence":"Medium","gaps":["Direct CDK1 binding not structurally shown","FOXO1 regulation mechanism incomplete"]},{"year":2014,"claim":"Linked Spy1 to growth-cone dynamics through CRMP1, implicating Spy1 in CDK5-mediated CRMP1 phosphorylation and Sema3A-induced collapse.","evidence":"Yeast two-hybrid, co-IP, overexpression/shRNA, growth-cone collapse assay, rat sciatic nerve crush","pmids":["25526860"],"confidence":"Low","gaps":["Single Co-IP plus limited mechanistic follow-up","How Spy1 modulates a CDK5-dependent event not defined"]},{"year":2015,"claim":"Identified a non-cell-cycle role in which Spy1 binds SCG10 and promotes its phosphorylation and proteasomal degradation, coupling Spy1 to axonal degeneration after nerve injury.","evidence":"Co-IP, in vitro binding, phosphorylation/degradation westerns, Spy1 inhibition with phenotypic rescue","pmids":["25869138"],"confidence":"Medium","gaps":["Direct kinase identity for SCG10 phosphorylation not fully resolved","Single lab"]},{"year":2015,"claim":"Showed Spy1 sequesters CLIPR-59 away from the deubiquitinase CYLD, controlling RIP1 K63-ubiquitination and TNF-α-induced apoptosis in glioblastoma, revealing a scaffold-type role distinct from CDK activation.","evidence":"Co-IP, siRNA, ubiquitination and caspase activity assays","pmids":["26017671"],"confidence":"Medium","gaps":["Structural basis of CLIPR-59 binding unknown","Single lab"]},{"year":2016,"claim":"Genetically separated Spy1's CDK2- and p27-binding surfaces, showing both contribute to proliferation and tumorigenesis but only p27 binding is required for p27 destabilisation.","evidence":"Site-directed mutagenesis, co-IP, CDK2 kinase and p27 stability assays, in vivo tumour model","pmids":["26771716"],"confidence":"Medium","gaps":["Did not provide atomic-resolution view of the two interfaces","Single lab"]},{"year":2017,"claim":"Provided the structural mechanism: crystal structures of CDK2-Spy1 and p27-CDK2-Spy1 explain phosphorylation-independent activation, p27 resistance, and altered substrate specificity arising from absence of the cyclin-binding groove.","evidence":"X-ray crystallography of two complexes, in vitro kinase assay, mutagenesis, proliferation assay","pmids":["28666995"],"confidence":"High","gaps":["Substrate-specificity rules not exhaustively mapped","No structure of Spy1-CDK1 complex"]},{"year":2017,"claim":"Connected Spy1 to MEK-independent ERK1/2 activation that drives ligand-independent ERα activation and tamoxifen resistance, adding a kinase-signalling output to Spy1 biology.","evidence":"ERK1/2 and ERα phosphorylation assays, MEK inhibitor controls, tamoxifen sensitivity, overexpression/knockdown","pmids":["28423577"],"confidence":"Medium","gaps":["Direct mechanism of MEK-independent ERK activation undefined","Single lab"]},{"year":2019,"claim":"Defined upstream control of Spy1 abundance, showing p53 directs Nedd4-mediated proteasomal degradation of Spy1 and that p53 loss permits Spy1 accumulation and mammary tumorigenesis.","evidence":"Transgenic mouse, protein stability assays, Nedd4 co-IP/ubiquitination, p53 KO/mutation analysis","pmids":["31829284"],"confidence":"Medium","gaps":["Nedd4 recognition motif on Spy1 not mapped","Single lab"]},{"year":2020,"claim":"Revealed a meiotic role: SPDYA binds SUN1 at the nuclear envelope through its Ringo domain and recruits CDK2 near the MAJIN-binding site, supporting telomere-nuclear envelope attachment.","evidence":"Co-IP, domain mapping, CDK2 inhibitor treatment, binding-site mutagenesis","pmids":["33015044"],"confidence":"Medium","gaps":["In vivo meiotic requirement not yet tested at this stage","CDK2 substrates at the LINC complex unknown"]},{"year":2021,"claim":"Established structurally and genetically that the SUN1-SPDYA-CDK2 complex organises telomere supramolecular architecture and is required for homologous pairing and synapsis in meiosis prophase I.","evidence":"X-ray crystallography of ternary complex, SUN1 mutagenesis, SPDYA-binding-deficient SUN1 knockin mouse, meiotic phenotyping","pmids":["34039995"],"confidence":"High","gaps":["Direct CDK2 phosphorylation targets driving telomere attachment not identified"]},{"year":2021,"claim":"Showed SPY1 activates EZH2/H3K27me3 to silence CDKN1A/CDKN2A and override senescence, making SPY1 a required factor for efficient somatic-cell reprogramming.","evidence":"iPSC reprogramming assay, EZH2/H3K27me3 westerns, knockdown/overexpression, CDK inhibitor expression analysis","pmids":["34486784"],"confidence":"Medium","gaps":["Mechanism by which SPY1 activates EZH2 undefined","Single lab"]},{"year":2022,"claim":"Implicated Spy1 in neuroprotection, showing MDM2-mediated degradation of Spy1 in ALS neurons and that Spy1 overexpression suppresses ferroptosis via the GCH1/BH4 axis and reduced TFR1-mediated iron import, delaying disease in mice.","evidence":"Ubiquitination assay, MDM2 manipulation, lipid peroxidation and GCH1/TFR1 readouts, ALS transgenic mouse","pmids":["36443440"],"confidence":"Medium","gaps":["Direct link between Spy1 and GCH1/TFR1 regulation not biochemically defined","Single lab"]},{"year":2022,"claim":"Correlated Spy1 with c-Myc protein stabilisation in triple-negative breast cancer and chemoresistance, but without defining the stabilisation mechanism.","evidence":"shRNA knockdown, c-Myc protein westerns, chemotherapy sensitivity assays, tissue microarray","pmids":["36029387"],"confidence":"Low","gaps":["Mechanism of c-Myc stabilisation not biochemically defined","Co-regulation observed without direct binding evidence"]},{"year":2023,"claim":"Demonstrated in vivo that RingoA sets a CDK activity threshold governing exit of adult neural stem cells from quiescence, with deficiency causing quiescent-NSC accumulation and reduced olfactory neurogenesis.","evidence":"RingoA knockout mouse, CDK activity assays, neurogenesis quantification","pmids":["36876138"],"confidence":"Medium","gaps":["Specific CDK partner and substrates in NSCs not defined","Single lab"]},{"year":null,"claim":"It remains unresolved which CDK2 substrates at the SUN1-LINC complex execute telomere-nuclear envelope attachment, and how the same atypical activator selects between cell-cycle, signalling, epigenetic, and scaffolding outputs in different tissues.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No meiotic CDK2 substrate identified","Mechanism of context-dependent output switching unknown","No structure of a Spy1-CDK1 complex"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,3,9]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,3,9]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[9,13]}],"localization":[{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[12,13]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3,14]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,3,9]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[2,4]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[12,13]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[2,7,15]}],"complexes":["CDK2-Spy1 complex","p27-CDK2-Spy1 complex","SUN1-SPDYA-CDK2 complex"],"partners":["CDK2","CDKN1B","CDK1","SUN1","STMN2","NEDD4","MDM2","CLIP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5MJ70","full_name":"Speedy protein A","aliases":["Rapid inducer of G2/M progression in oocytes A","RINGO A","hSpy/Ringo A","Speedy-1","Spy1"],"length_aa":313,"mass_kda":36.5,"function":"Regulates the G1/S phase transition of the cell cycle by binding and activating CDK1 and CDK2 (PubMed:12972555). Contributes to CDK2 activation without promoting CDK2 phosphorylation, by inducing a conformation change of the CDK2 T-loop that obstructs the substrate-binding cleft prior to kinase activation (PubMed:28666995). Mediates cell survival during the DNA damage process through activation of CDK2 (PubMed:12839962)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q5MJ70/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SPDYA","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SPDYA","total_profiled":1310},"omim":[{"mim_id":"621172","title":"RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 39; ARHGEF39","url":"https://www.omim.org/entry/621172"},{"mim_id":"614030","title":"SPEEDY/RINGO CELL CYCLE REGULATOR FAMILY, MEMBER C; SPDYC","url":"https://www.omim.org/entry/614030"},{"mim_id":"614029","title":"SPEEDY/RINGO CELL CYCLE REGULATOR FAMILY, MEMBER A; SPDYA","url":"https://www.omim.org/entry/614029"},{"mim_id":"607342","title":"CYTOPLASMIC POLYADENYLATION ELEMENT-BINDING PROTEIN 1; CPEB1","url":"https://www.omim.org/entry/607342"},{"mim_id":"176948","title":"MITOGEN-ACTIVATED PROTEIN KINASE 1; MAPK1","url":"https://www.omim.org/entry/176948"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"testis","ntpm":30.8}],"url":"https://www.proteinatlas.org/search/SPDYA"},"hgnc":{"alias_symbol":["SPY1","Ringo3"],"prev_symbol":["SPDY1"]},"alphafold":{"accession":"Q5MJ70","domains":[{"cath_id":"-","chopping":"79-199","consensus_level":"medium","plddt":95.3206,"start":79,"end":199}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5MJ70","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5MJ70-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5MJ70-F1-predicted_aligned_error_v6.png","plddt_mean":68.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SPDYA","jax_strain_url":"https://www.jax.org/strain/search?query=SPDYA"},"sequence":{"accession":"Q5MJ70","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5MJ70.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5MJ70/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5MJ70"}},"corpus_meta":[{"pmid":"36443440","id":"PMC_36443440","title":"SPY1 inhibits neuronal ferroptosis in amyotrophic lateral sclerosis by reducing lipid peroxidation through regulation of GCH1 and TFR1.","date":"2022","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/36443440","citation_count":136,"is_preprint":false},{"pmid":"12972555","id":"PMC_12972555","title":"Spy1 interacts with p27Kip1 to allow G1/S progression.","date":"2003","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/12972555","citation_count":44,"is_preprint":false},{"pmid":"10940030","id":"PMC_10940030","title":"Spy1, a histidine-containing phosphotransfer signaling protein, regulates the fission yeast cell cycle through the Mcs4 response regulator.","date":"2000","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/10940030","citation_count":38,"is_preprint":false},{"pmid":"12839962","id":"PMC_12839962","title":"Human Spy1 promotes survival of mammalian cells following DNA 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resistance in multiple myeloma cells.","date":"2013","source":"International journal of hematology","url":"https://pubmed.ncbi.nlm.nih.gov/24037419","citation_count":16,"is_preprint":false},{"pmid":"22447439","id":"PMC_22447439","title":"Spy1 is frequently overexpressed in malignant gliomas and critically regulates the proliferation of glioma cells.","date":"2012","source":"Journal of molecular neuroscience : MN","url":"https://pubmed.ncbi.nlm.nih.gov/22447439","citation_count":16,"is_preprint":false},{"pmid":"25594028","id":"PMC_25594028","title":"The atypical cell cycle regulator Spy1 suppresses differentiation of the neuroblastoma stem cell population.","date":"2014","source":"Oncoscience","url":"https://pubmed.ncbi.nlm.nih.gov/25594028","citation_count":16,"is_preprint":false},{"pmid":"33015044","id":"PMC_33015044","title":"Tethering of Telomeres to the Nuclear Envelope Is Mediated by SUN1-MAJIN and Possibly Promoted by SPDYA-CDK2 During Meiosis.","date":"2020","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/33015044","citation_count":15,"is_preprint":false},{"pmid":"30116243","id":"PMC_30116243","title":"Protective Regulatory T Cell Immune Response Induced by Intranasal Immunization With the Live-Attenuated Pneumococcal Vaccine SPY1 via the Transforming Growth Factor-β1-Smad2/3 Pathway.","date":"2018","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30116243","citation_count":15,"is_preprint":false},{"pmid":"25312946","id":"PMC_25312946","title":"Mucosal immunization with the live attenuated vaccine SPY1 induces humoral and Th2-Th17-regulatory T cell cellular immunity and protects against pneumococcal infection.","date":"2014","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/25312946","citation_count":15,"is_preprint":false},{"pmid":"26644004","id":"PMC_26644004","title":"Spy1 participates in the proliferation and apoptosis of epithelial ovarian cancer.","date":"2015","source":"Journal of molecular histology","url":"https://pubmed.ncbi.nlm.nih.gov/26644004","citation_count":13,"is_preprint":false},{"pmid":"31829284","id":"PMC_31829284","title":"The atypical cyclin-like protein Spy1 overrides p53-mediated tumour suppression and promotes susceptibility to breast tumourigenesis.","date":"2019","source":"Breast cancer research : BCR","url":"https://pubmed.ncbi.nlm.nih.gov/31829284","citation_count":12,"is_preprint":false},{"pmid":"28423577","id":"PMC_28423577","title":"The cyclin-like protein, SPY1, regulates the ERα and ERK1/2 pathways promoting tamoxifen resistance.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/28423577","citation_count":12,"is_preprint":false},{"pmid":"19082704","id":"PMC_19082704","title":"Peripheral nerve lesion induces an up-regulation of Spy1 in rat spinal cord.","date":"2008","source":"Cellular and molecular neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/19082704","citation_count":12,"is_preprint":false},{"pmid":"26771716","id":"PMC_26771716","title":"Direct interactions with both p27 and Cdk2 regulate Spy1-mediated proliferation in vivo and in vitro.","date":"2016","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/26771716","citation_count":10,"is_preprint":false},{"pmid":"25869138","id":"PMC_25869138","title":"Spy1 Protein Mediates Phosphorylation and Degradation of SCG10 Protein in Axonal Degeneration.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/25869138","citation_count":8,"is_preprint":false},{"pmid":"22573156","id":"PMC_22573156","title":"Isolation and functional analysis of spy1 responsible for pristinamycin yield in Streptomyces pristinaespiralis.","date":"2012","source":"Journal of microbiology and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/22573156","citation_count":8,"is_preprint":false},{"pmid":"36029387","id":"PMC_36029387","title":"Stabilization of c-Myc by the atypical cell cycle regulator, Spy1, decreases efficacy of breast cancer treatments.","date":"2022","source":"Breast cancer research and treatment","url":"https://pubmed.ncbi.nlm.nih.gov/36029387","citation_count":7,"is_preprint":false},{"pmid":"27609353","id":"PMC_27609353","title":"Attenuated Streptococcus pneumoniae vaccine candidate SPY1 promotes dendritic cell activation and drives a Th1/Th17 response.","date":"2016","source":"Immunology letters","url":"https://pubmed.ncbi.nlm.nih.gov/27609353","citation_count":6,"is_preprint":false},{"pmid":"20563653","id":"PMC_20563653","title":"Protective roles and Pap1-dependent regulation of the Schizosaccharomyces pombe spy1 gene under nitrosative and nutritional stresses.","date":"2010","source":"Molecular biology 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Korea)","url":"https://pubmed.ncbi.nlm.nih.gov/28956354","citation_count":5,"is_preprint":false},{"pmid":"34486784","id":"PMC_34486784","title":"The cyclin-like protein SPY1 overrides reprogramming induced senescence through EZH2 mediated H3K27me3.","date":"2021","source":"Stem cells (Dayton, Ohio)","url":"https://pubmed.ncbi.nlm.nih.gov/34486784","citation_count":4,"is_preprint":false},{"pmid":"37588169","id":"PMC_37588169","title":"IL-27 mediates immune response of pneumococcal vaccine SPY1 through Th17 and memory CD4+T cells.","date":"2023","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/37588169","citation_count":3,"is_preprint":false},{"pmid":"40034037","id":"PMC_40034037","title":"Targeting cyclin-dependent kinase 2 (CDK2) interactions with cyclins and Speedy 1 (Spy1) for cancer and male contraception.","date":"2025","source":"Future medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40034037","citation_count":2,"is_preprint":false},{"pmid":"26563004","id":"PMC_26563004","title":"[Identification of a point mutation in the promoter region of cps operon responsible for capsular polysaccharide deficiency in Streptococcus pneumniae SPY1].","date":"2015","source":"Wei sheng wu xue bao = Acta microbiologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/26563004","citation_count":1,"is_preprint":false},{"pmid":"24596205","id":"PMC_24596205","title":"SPY1-mediated symmetric cell division promotes BTIC self-renewal.","date":"2014","source":"Cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/24596205","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19908,"output_tokens":5015,"usd":0.067475,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13310,"output_tokens":5725,"usd":0.104838,"stage2_stop_reason":"end_turn"},"total_usd":0.172313,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2003,\n      \"finding\": \"Spy1 directly interacts with the CDK inhibitor p27Kip1 (confirmed by yeast two-hybrid, in vitro pulldown with bacterially expressed proteins, and co-immunoprecipitation of endogenous and transfected proteins in mammalian cells), and this interaction allows Spy1 to overcome p27-induced G1 arrest to promote CDK2-dependent DNA synthesis; proliferative effects of Spy1 require endogenous p27.\",\n      \"method\": \"Yeast two-hybrid screen, in vitro pulldown (bacterially expressed proteins), co-immunoprecipitation, CDK2 histone H1 kinase assay, p27-null cell rescue experiments\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (Y2H, in vitro pulldown, co-IP, kinase assay, genetic rescue) in one study, subsequently replicated by other labs\",\n      \"pmids\": [\"12972555\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Human Spy1 binds and activates CDK2 during the DNA damage response; Spy1 overexpression enhances cell viability after genotoxic damage (camptothecin, cisplatin, hydroxyurea), and a dominant-negative CDK2 overrides Spy1 function, demonstrating that CDK2 activation is required for Spy1-mediated cell survival.\",\n      \"method\": \"Clonogenic survival assays, comet assays, dominant-negative CDK2 expression, siRNA knockdown, endogenous protein level analysis by western blot\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — dominant-negative epistasis and siRNA knockdown with multiple damage readouts, single lab\",\n      \"pmids\": [\"12839962\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Spy1 expression suppresses UV-induced caspase-3 activation and apoptosis, allows UV-irradiation-resistant DNA synthesis and mitotic entry (histone H3 phosphorylation), and inhibits phosphorylation of Chk1, RPA, and histone H2A.X; mutation of the conserved Speedy/Ringo box (CDK2-interaction domain) abrogates these effects, placing CDK2 activation upstream of checkpoint bypass and apoptosis suppression.\",\n      \"method\": \"Inducible Spy1 expression system, flow cytometry, western blot for checkpoint markers, Speedy/Ringo box point mutant\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — inducible system with mutagenesis and multiple orthogonal readouts, single lab\",\n      \"pmids\": [\"16951407\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Spy1 activates CDK2 to phosphorylate p27Kip1 at T187 in vitro using recombinant proteins; Spy1/CDK2 added to a preformed inhibited cyclin E/CDK2/p27 complex promotes T187 phosphorylation; in cells, inducible Spy1 expression reduces endogenous p27 and exogenous p27WT but not p27T187A, and synchronised cells show enhanced T187 phosphorylation and p27 degradation in late G1 and S-phase.\",\n      \"method\": \"In vitro kinase assay with recombinant proteins, inducible expression system, synchronized HeLa cell analysis, T187A mutant control, western blot\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstituted in vitro kinase assay plus cell-based mutagenesis validation, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"17671428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Spy1-mediated inhibition of apoptosis and bypass of UV-induced checkpoint activation requires the presence of functional p53 and the CDK inhibitor p21; Spy1 expression prevents nucleotide excision repair of cyclobutane pyrimidine dimers, increases cellular mutation frequency, reduces cyclin E-induced γH2A.X foci formation, and knockdown of endogenous Spy1 itself leads to γH2A.X foci, Chk1 phosphorylation, and proliferation defects.\",\n      \"method\": \"siRNA knockdown, p53/p21 genetic requirement analysis, CPD repair assay, mutation frequency assay, γH2A.X and Chk1 phosphorylation western blot\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis with p53/p21, endogenous knockdown with multiple readouts, single lab\",\n      \"pmids\": [\"19106603\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Spy1 facilitates mammary cell transformation in a manner dependent on activation of CDK1, with subsequent inhibition of the anti-apoptotic regulator FOXO1; knockdown of Spy1 impairs breast cancer cell proliferation.\",\n      \"method\": \"CDK1 activity assays, FOXO1 functional analysis, shRNA knockdown, in vivo mouse mammary tumor model\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — CDK1 and FOXO1 mechanistic follow-up with in vivo support, single lab\",\n      \"pmids\": [\"22280365\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Spy1 directly binds SCG10 (a microtubule-destabilising protein/axonal maintenance factor) and mediates SCG10 phosphorylation and proteasomal degradation in a partially JNK-dependent manner following sciatic nerve injury; inhibition of Spy1 attenuates SCG10 phosphorylation and delays axonal degeneration.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assay, western blot for phosphorylation/degradation, Spy1 inhibition with phenotypic rescue\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — co-IP plus functional inhibition with defined pathway placement, single lab\",\n      \"pmids\": [\"25869138\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Spy1 interacts with CLIPR-59 in glioblastoma cells, sequestering CLIPR-59 away from CYLD (a K63-deubiquitinase); knockdown of Spy1 increases CLIPR-59-CYLD association, enhances K63-deubiquitination of RIP1, and promotes caspase-8/caspase-3 activation, thereby sensitising GBM cells to TNF-α-induced apoptosis.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, ubiquitination assay, caspase activity assays, western blot\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — co-IP plus mechanistic epistasis, single lab\",\n      \"pmids\": [\"26017671\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Specific residues in Spy1 mediate direct interaction with CDK2 and separately with p27Kip1; point mutations disrupting each interaction reduce endogenous CDK2 activity and Spy1-mediated proliferation; only the p27-interaction mutation abolishes Spy1-mediated p27 destabilisation, while disruption of either interaction slows Spy1-driven tumorigenesis in vivo.\",\n      \"method\": \"Site-directed mutagenesis, co-immunoprecipitation, CDK2 kinase assay, p27 stability assay, in vivo mouse tumour model\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — mutagenesis with biochemical and in vivo validation, single lab\",\n      \"pmids\": [\"26771716\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structures of the Cdk2-Spy1 binary complex and the p27-Cdk2-Spy1 ternary complex reveal that Spy1 activates Cdk2 by inducing structural changes that bypass the requirement for activation-loop phosphorylation; Spy1 lacks the cyclin-binding groove that mediates p27 inhibition and substrate cyclin-docking, explaining why Cdk-Spy1 complexes are resistant to p27 and have altered substrate specificity; Spy1 mutations that ablate Cdk2 binding also abolish cell proliferation.\",\n      \"method\": \"X-ray crystallography, in vitro CDK2 kinase assay, site-directed mutagenesis, cell proliferation assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures of two complexes with mutagenesis and functional validation, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"28666995\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Spy1 activates ERK1/2 in a MEK-independent manner; Spy1-mediated ERK activation increases ligand-independent phosphorylation and activation of estrogen receptor α, correlating with decreased tamoxifen sensitivity in breast cancer cells.\",\n      \"method\": \"ERK1/2 phosphorylation assays, MEK inhibitor controls, ERα phosphorylation assays, tamoxifen sensitivity assays, Spy1 overexpression/knockdown\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — pharmacological epistasis with MEK inhibitor and ERα phosphorylation readout, single lab\",\n      \"pmids\": [\"28423577\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"p53 controls Spy1 protein levels via proteasomal degradation mediated in part by the E3 ubiquitin ligase Nedd4; loss or mutation of p53 allows Spy1 accumulation, leading to mammary hyperplasia; in a transgenic mouse model, sustained Spy1 elevation results in increased mammary proliferation and tumour susceptibility.\",\n      \"method\": \"Transgenic mouse model, in vitro protein stability assays, Nedd4 co-immunoprecipitation/ubiquitination, p53 knockout/mutation analysis\",\n      \"journal\": \"Breast cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Nedd4-mediated ubiquitination supported by co-IP and in vivo transgenic model, single lab\",\n      \"pmids\": [\"31829284\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"SPDYA (Speedy A) directly interacts with SUN1 at the nuclear envelope via its Ringo domain and recruits CDK2 to SUN1; the SPDYA-binding site on SUN1 is in the N-terminal domain, close to the MAJIN-binding site; CDK2 inhibitors decrease the SUN1-MAJIN interaction, suggesting SPDYA-CDK2 promotes telomere-nuclear envelope attachment during meiosis.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping experiments, CDK2 inhibitor treatment, binding-site mutagenesis\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — co-IP and domain mapping with pharmacological epistasis, single lab\",\n      \"pmids\": [\"33015044\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SPDYA directly interacts with SUN1; the crystal structure of the human SUN1-SPDYA-CDK2 ternary complex was determined; SUN1 mutations that disrupt SPDYA binding in mice impair telomere-LINC complex attachment, abolish the ring-shaped telomere supramolecular architecture at the nuclear envelope, and cause defects in homologous pairing and synapsis during meiosis prophase I.\",\n      \"method\": \"X-ray crystallography (ternary complex), site-directed mutagenesis of SUN1, mouse genetic model (SPDYA-binding-deficient SUN1 knockin), meiosis phenotype analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure of ternary complex combined with in vivo mouse genetic validation, multiple orthogonal methods in single rigorous study\",\n      \"pmids\": [\"34039995\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SPY1 activates the epigenetic regulator EZH2 to promote H3K27me3-mediated repression of CDK inhibitors CDKN1A and CDKN2A, overriding senescence during reprogramming; SPY1 is required for efficient reprogramming of mouse fibroblasts to induced pluripotent stem cells.\",\n      \"method\": \"iPSC reprogramming assay, EZH2 activity/H3K27me3 western blot, Spy1 knockdown/overexpression, CDKN1A/CDKN2A expression analysis\",\n      \"journal\": \"Stem cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — functional reprogramming assay with epigenetic readout, single lab\",\n      \"pmids\": [\"34486784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SPY1 protein is degraded via ubiquitination mediated by MDM2 (an E3 ubiquitin ligase) in ALS motor neurons; overexpression of Spy1 suppresses ferroptosis in hSOD1G93A cells by restoring the GCH1/BH4 axis (a ferroptosis resistance pathway) and reducing TFR1-mediated iron import, decreasing lipid peroxidation; neuron-specific Spy1 overexpression delays disease onset and extends survival in ALS transgenic mice.\",\n      \"method\": \"Ubiquitination assay, MDM2 knockdown/overexpression, lipid peroxidation measurement, GCH1/TFR1 western blot and activity assays, transgenic mouse model with neurological scoring\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination assay plus in vivo mouse model with mechanistic pathway analysis, single lab\",\n      \"pmids\": [\"36443440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Spy1 stabilises c-Myc protein in TNBC cells; knockdown of Spy1 reduces c-Myc protein levels and sensitises TNBC cells to chemotherapy; Spy1 protein levels positively correlate with c-Myc protein (not mRNA) levels in TNBC patient samples.\",\n      \"method\": \"shRNA knockdown, western blot for c-Myc protein, chemotherapy sensitivity assays, tissue microarray\",\n      \"journal\": \"Breast cancer research and treatment\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-regulation observed by knockdown and protein correlation, mechanism of stabilisation not biochemically defined, single lab\",\n      \"pmids\": [\"36029387\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RingoA (Spy1 ortholog in mouse) regulates exit from quiescence in adult neural stem cells; RingoA expression increases CDK activity and facilitates cell cycle entry; RingoA-deficient mice show reduced olfactory neurogenesis and accumulation of quiescent NSCs, placing RingoA as a CDK activity threshold regulator for NSC quiescence-to-activation transition.\",\n      \"method\": \"RingoA knockout mouse, CDK activity assays, neurogenesis quantification, quiescent NSC accumulation analysis\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO mouse with CDK activity and neurogenesis phenotypes, single lab\",\n      \"pmids\": [\"36876138\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CRMP1 interacts with Spy1 (identified by yeast two-hybrid and confirmed by co-IP); Spy1 affects CDK5-mediated CRMP1 phosphorylation, which disrupts CRMP1-actin association and contributes to Sema3A-induced growth cone collapse and impaired regeneration after sciatic nerve crush.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, overexpression/shRNA, CRMP1 phosphorylation assay, growth cone collapse assay, rat sciatic nerve crush model\",\n      \"journal\": \"Molecular neurobiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, co-IP plus limited mechanistic follow-up of CDK5-CRMP1 phosphorylation axis\",\n      \"pmids\": [\"25526860\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SPDYA (Spy1) is an atypical 'cyclin-like' CDK activator that binds and activates CDK2 (and CDK1) through a structurally distinct mechanism—confirmed by crystal structures of the CDK2-Spy1 and p27-CDK2-Spy1 complexes—that confers activation-loop-phosphorylation independence and resistance to p27 inhibition; Spy1 promotes G1/S progression by directly binding p27Kip1 and stimulating CDK2-mediated p27-T187 phosphorylation and degradation, bypasses DNA-damage checkpoints and apoptosis through CDK2 in a p53/p21-dependent context, is itself degraded by the MDM2 and Nedd4 E3 ubiquitin ligases, activates ERK1/2 in a MEK-independent manner to drive ERα signalling, stabilises c-Myc, activates EZH2-mediated H3K27me3 to silence CDK inhibitors during reprogramming, interacts with SUN1 at the nuclear envelope via its Ringo domain to recruit CDK2 and support telomere attachment during meiosis prophase I, and regulates neural stem cell quiescence exit as well as axonal degeneration through SCG10 phosphorylation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SPDYA (Spy1/RingoA) is an atypical, cyclin-like activator of cyclin-dependent kinases that drives cell-cycle entry and proliferation through a structurally distinct mechanism of CDK2/CDK1 activation [#0, #9]. Crystal structures of the CDK2-Spy1 binary and p27-CDK2-Spy1 ternary complexes show that Spy1 induces conformational changes that activate CDK2 independently of activation-loop phosphorylation, and that Spy1 lacks the cyclin-binding groove, rendering Spy1-CDK2 complexes resistant to p27 inhibition and altering substrate specificity [#9]. Spy1 directly binds the CDK inhibitor p27Kip1 through residues separable from its CDK2-interaction surface, and stimulates CDK2-mediated phosphorylation of p27 at T187, triggering its degradation to overcome p27-induced G1 arrest and promote S-phase entry [#0, #3, #8]. Through CDK2 activation Spy1 suppresses DNA-damage checkpoints and apoptosis in a p53/p21-dependent context, permitting damage-resistant DNA synthesis and mitotic entry while impairing repair fidelity [#1, #2, #4]. Spy1 promotes mammary transformation via CDK1 activation and FOXO1 inhibition, activates ERK1/2 in a MEK-independent manner to drive ligand-independent ERα signalling and tamoxifen resistance, and engages epigenetic silencing of CDK inhibitors via EZH2/H3K27me3 to override senescence during reprogramming [#5, #10, #14]. Spy1 protein abundance is controlled by proteasomal degradation through the E3 ligases Nedd4 (downstream of p53) and MDM2 [#11, #15]. Beyond cell-cycle control, Spy1 uses its Ringo domain to bind SUN1 at the nuclear envelope and recruit CDK2 to support telomere-LINC complex attachment, homologous pairing and synapsis during meiosis prophase I [#12, #13], and regulates neural stem-cell exit from quiescence as a CDK activity threshold setter [#17].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established that Spy1 physically binds the CDK inhibitor p27Kip1 and uses this interaction to bypass p27-imposed G1 arrest, defining a mechanism by which Spy1 overrides a key proliferation brake.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro pulldown, co-IP, CDK2 H1 kinase assay, and p27-null rescue in mammalian cells\",\n      \"pmids\": [\"12972555\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether Spy1 phosphorylates p27 directly or via CDK2\", \"Structural basis of p27 binding unresolved\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Showed Spy1 binds and activates CDK2 to promote survival after genotoxic damage, with dominant-negative CDK2 abolishing the effect, placing CDK2 activation as the required effector of Spy1-mediated cell survival.\",\n      \"evidence\": \"Clonogenic and comet assays, dominant-negative CDK2, siRNA knockdown across multiple damaging agents\",\n      \"pmids\": [\"12839962\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Did not define which checkpoint nodes are bypassed\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstrated that Spy1 suppresses UV-induced apoptosis and checkpoint signalling (Chk1, RPA, H2A.X) in a manner dependent on the Speedy/Ringo box, placing CDK2 activation upstream of checkpoint bypass.\",\n      \"evidence\": \"Inducible Spy1 expression, flow cytometry, checkpoint-marker westerns, Ringo-box point mutant\",\n      \"pmids\": [\"16951407\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of checkpoint suppression not biochemically dissected\", \"Single lab\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Reconstituted the biochemical core of Spy1 function by showing Spy1/CDK2 phosphorylates p27 at T187 in vitro and drives T187-dependent p27 degradation in cells, linking Spy1 directly to controlled p27 turnover.\",\n      \"evidence\": \"In vitro kinase assay with recombinant proteins, inducible expression, synchronized HeLa cells, T187A mutant control\",\n      \"pmids\": [\"17671428\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the ubiquitin ligase acting on phospho-T187 p27 in this context\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined the genetic context of checkpoint bypass, showing Spy1's anti-apoptotic and checkpoint-overriding effects require functional p53 and p21 and come at the cost of impaired excision repair and increased mutation frequency.\",\n      \"evidence\": \"siRNA knockdown, p53/p21 requirement analysis, CPD repair and mutation-frequency assays, γH2A.X/Chk1 westerns\",\n      \"pmids\": [\"19106603\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic basis of repair inhibition unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Extended Spy1's transforming role to CDK1, showing mammary transformation depends on CDK1 activation and FOXO1 inhibition, broadening Spy1's CDK targets beyond CDK2.\",\n      \"evidence\": \"CDK1 activity assays, FOXO1 analysis, shRNA, in vivo mouse mammary tumor model\",\n      \"pmids\": [\"22280365\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct CDK1 binding not structurally shown\", \"FOXO1 regulation mechanism incomplete\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked Spy1 to growth-cone dynamics through CRMP1, implicating Spy1 in CDK5-mediated CRMP1 phosphorylation and Sema3A-induced collapse.\",\n      \"evidence\": \"Yeast two-hybrid, co-IP, overexpression/shRNA, growth-cone collapse assay, rat sciatic nerve crush\",\n      \"pmids\": [\"25526860\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP plus limited mechanistic follow-up\", \"How Spy1 modulates a CDK5-dependent event not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identified a non-cell-cycle role in which Spy1 binds SCG10 and promotes its phosphorylation and proteasomal degradation, coupling Spy1 to axonal degeneration after nerve injury.\",\n      \"evidence\": \"Co-IP, in vitro binding, phosphorylation/degradation westerns, Spy1 inhibition with phenotypic rescue\",\n      \"pmids\": [\"25869138\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct kinase identity for SCG10 phosphorylation not fully resolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed Spy1 sequesters CLIPR-59 away from the deubiquitinase CYLD, controlling RIP1 K63-ubiquitination and TNF-α-induced apoptosis in glioblastoma, revealing a scaffold-type role distinct from CDK activation.\",\n      \"evidence\": \"Co-IP, siRNA, ubiquitination and caspase activity assays\",\n      \"pmids\": [\"26017671\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of CLIPR-59 binding unknown\", \"Single lab\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Genetically separated Spy1's CDK2- and p27-binding surfaces, showing both contribute to proliferation and tumorigenesis but only p27 binding is required for p27 destabilisation.\",\n      \"evidence\": \"Site-directed mutagenesis, co-IP, CDK2 kinase and p27 stability assays, in vivo tumour model\",\n      \"pmids\": [\"26771716\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not provide atomic-resolution view of the two interfaces\", \"Single lab\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Provided the structural mechanism: crystal structures of CDK2-Spy1 and p27-CDK2-Spy1 explain phosphorylation-independent activation, p27 resistance, and altered substrate specificity arising from absence of the cyclin-binding groove.\",\n      \"evidence\": \"X-ray crystallography of two complexes, in vitro kinase assay, mutagenesis, proliferation assay\",\n      \"pmids\": [\"28666995\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate-specificity rules not exhaustively mapped\", \"No structure of Spy1-CDK1 complex\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected Spy1 to MEK-independent ERK1/2 activation that drives ligand-independent ERα activation and tamoxifen resistance, adding a kinase-signalling output to Spy1 biology.\",\n      \"evidence\": \"ERK1/2 and ERα phosphorylation assays, MEK inhibitor controls, tamoxifen sensitivity, overexpression/knockdown\",\n      \"pmids\": [\"28423577\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mechanism of MEK-independent ERK activation undefined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined upstream control of Spy1 abundance, showing p53 directs Nedd4-mediated proteasomal degradation of Spy1 and that p53 loss permits Spy1 accumulation and mammary tumorigenesis.\",\n      \"evidence\": \"Transgenic mouse, protein stability assays, Nedd4 co-IP/ubiquitination, p53 KO/mutation analysis\",\n      \"pmids\": [\"31829284\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Nedd4 recognition motif on Spy1 not mapped\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed a meiotic role: SPDYA binds SUN1 at the nuclear envelope through its Ringo domain and recruits CDK2 near the MAJIN-binding site, supporting telomere-nuclear envelope attachment.\",\n      \"evidence\": \"Co-IP, domain mapping, CDK2 inhibitor treatment, binding-site mutagenesis\",\n      \"pmids\": [\"33015044\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo meiotic requirement not yet tested at this stage\", \"CDK2 substrates at the LINC complex unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established structurally and genetically that the SUN1-SPDYA-CDK2 complex organises telomere supramolecular architecture and is required for homologous pairing and synapsis in meiosis prophase I.\",\n      \"evidence\": \"X-ray crystallography of ternary complex, SUN1 mutagenesis, SPDYA-binding-deficient SUN1 knockin mouse, meiotic phenotyping\",\n      \"pmids\": [\"34039995\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct CDK2 phosphorylation targets driving telomere attachment not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed SPY1 activates EZH2/H3K27me3 to silence CDKN1A/CDKN2A and override senescence, making SPY1 a required factor for efficient somatic-cell reprogramming.\",\n      \"evidence\": \"iPSC reprogramming assay, EZH2/H3K27me3 westerns, knockdown/overexpression, CDK inhibitor expression analysis\",\n      \"pmids\": [\"34486784\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which SPY1 activates EZH2 undefined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated Spy1 in neuroprotection, showing MDM2-mediated degradation of Spy1 in ALS neurons and that Spy1 overexpression suppresses ferroptosis via the GCH1/BH4 axis and reduced TFR1-mediated iron import, delaying disease in mice.\",\n      \"evidence\": \"Ubiquitination assay, MDM2 manipulation, lipid peroxidation and GCH1/TFR1 readouts, ALS transgenic mouse\",\n      \"pmids\": [\"36443440\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct link between Spy1 and GCH1/TFR1 regulation not biochemically defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Correlated Spy1 with c-Myc protein stabilisation in triple-negative breast cancer and chemoresistance, but without defining the stabilisation mechanism.\",\n      \"evidence\": \"shRNA knockdown, c-Myc protein westerns, chemotherapy sensitivity assays, tissue microarray\",\n      \"pmids\": [\"36029387\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Mechanism of c-Myc stabilisation not biochemically defined\", \"Co-regulation observed without direct binding evidence\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated in vivo that RingoA sets a CDK activity threshold governing exit of adult neural stem cells from quiescence, with deficiency causing quiescent-NSC accumulation and reduced olfactory neurogenesis.\",\n      \"evidence\": \"RingoA knockout mouse, CDK activity assays, neurogenesis quantification\",\n      \"pmids\": [\"36876138\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific CDK partner and substrates in NSCs not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved which CDK2 substrates at the SUN1-LINC complex execute telomere-nuclear envelope attachment, and how the same atypical activator selects between cell-cycle, signalling, epigenetic, and scaffolding outputs in different tissues.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No meiotic CDK2 substrate identified\", \"Mechanism of context-dependent output switching unknown\", \"No structure of a Spy1-CDK1 complex\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 3, 9]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 3, 9]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [9, 13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [12, 13]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 3, 9]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [12, 13]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [2, 7, 15]}\n    ],\n    \"complexes\": [\"CDK2-Spy1 complex\", \"p27-CDK2-Spy1 complex\", \"SUN1-SPDYA-CDK2 complex\"],\n    \"partners\": [\"CDK2\", \"CDKN1B\", \"CDK1\", \"SUN1\", \"STMN2\", \"NEDD4\", \"MDM2\", \"CLIP1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}