{"gene":"PSRC1","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":1999,"finding":"DDA3 (PSRC1) was identified as a p53-regulated gene: DDA3 mRNA is transcriptionally induced by p53 in a cycloheximide-insensitive, actinomycin D-sensitive manner, indicating direct transcriptional activation without requiring de novo protein synthesis. Overexpression of DDA3 suppressed colony formation in H1299 lung carcinoma cells.","method":"Differential mRNA display, actinomycin D/cycloheximide treatment, colony formation assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — transcriptional regulation demonstrated by pharmacological inhibitors and overexpression, single lab with two orthogonal methods","pmids":["10618717"],"is_preprint":false},{"year":2002,"finding":"Mouse DDA3 is a direct transcriptional target of both p53 and p73: a p53 response element (RE2) in the DDA3 gene was shown by luciferase reporter assay and gel mobility shift analysis to bind wild-type p53 and confer transactivation. DDA3 induction by DNA damage was absent in p53-knockout MEFs. p73 family members also transactivated DDA3 via RE2.","method":"Luciferase reporter assay, gel mobility shift assay, p53-knockout MEFs, overexpression","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (reporter assay, EMSA, KO cells) in single lab, replicated across p53 and p73","pmids":["12082536"],"is_preprint":false},{"year":2007,"finding":"DDA3 is a microtubule-associated protein that interacts with plus-end binding protein EB3. Interaction was confirmed by GST pull-down and co-immunoprecipitation (requiring intact microtubules). Interaction domains were mapped to DDA3 aa 118–241 and 242–329 (EB3 binding and MT-bundling) and EB3 N- and C-termini. DDA3 directly binds microtubules in vitro and cooperates with EB3 for MT binding. DDA3 also interacts with APC2. Ectopic expression of DDA3 and EB3 enhanced beta-catenin-dependent transactivation and cyclin D1; knockdown inhibited beta-catenin signaling and colony formation.","method":"Yeast two-hybrid, GST pull-down, co-immunoprecipitation, in vitro microtubule-binding assay, immunofluorescence, reporter assay, siRNA knockdown","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal biochemical methods (Y2H, GST pulldown, co-IP, in vitro MT binding, reporter), domain mapping, functional rescue","pmids":["17310996"],"is_preprint":false},{"year":2008,"finding":"Human DDA3 is transcriptionally repressed by p53 (opposite to mouse DDA3): p53 binds three consensus El-Deiry decamers at −1478/−1403 of the hDDA3 promoter as shown by chromatin immunoprecipitation, and luciferase analysis showed this region mediates p53-dependent repression. hDDA3 mRNA and protein are suppressed in DNA-damaged cells in a wild-type p53-dependent manner.","method":"Chromatin immunoprecipitation (ChIP), luciferase reporter assay, Western blot, real-time PCR","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — ChIP plus reporter assay with mutant p53 controls, multiple orthogonal methods in single study","pmids":["18291097"],"is_preprint":false},{"year":2008,"finding":"DDA3 recruits microtubule depolymerase Kif2a to the mitotic spindle and spindle poles in a microtubule-dependent manner. DDA3 depletion causes unaligned chromosomes, reduced inter-kinetochore tension, decreased anaphase chromosome velocity, increased spindle MT steady-state levels, reduced MT turnover, and increased MT polymerization rate — phenocopying partial Kif2a knockdown.","method":"siRNA depletion, mass spectrometry (co-purification), immunofluorescence, live imaging, fluorescence recovery after photobleaching (FRAP)","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — co-purification by MS, siRNA with multiple quantitative readouts (tension, velocity, FRAP), phenocopy experiment with Kif2a KD, replicated in multiple assays","pmids":["18411309"],"is_preprint":false},{"year":2008,"finding":"DDA3 interacts with ASPP2 (a p53-binding protein). The interaction domain on DDA3 maps to aa 118–241; both N- and C-terminal regions of ASPP2 bind DDA3. DDA3 dose-dependently inhibits ASPP2-stimulated p53-mediated BAX promoter activation without interfering with ASPP2–p53 binding.","method":"Yeast two-hybrid screening, GST pull-down, immunofluorescence colocalization, luciferase reporter assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — GST pulldown + reporter assay, domain mapping, single lab","pmids":["18793611"],"is_preprint":false},{"year":2009,"finding":"Domain analysis of DDA3: the C-terminal domain directly binds microtubules in vitro and associates with the mitotic spindle in vivo; the N-terminal domain does not bind MTs but acts dominant-negatively, preventing endogenous DDA3 spindle association and reducing spindle-associated Kif2a while increasing spindle MT density.","method":"In vitro microtubule-binding assay, dominant-negative overexpression, immunofluorescence, live imaging","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro MT binding, dominant-negative dissection, single lab with multiple readouts","pmids":["19738423"],"is_preprint":false},{"year":2010,"finding":"DDA3 is phosphorylated on Ser225 during mitosis. The phospho-mimicking S225D variant rescues DDA3-knockdown mitotic defects (unaligned chromosomes), whereas the non-phosphorylatable S225A mutant does not, demonstrating that Ser225 phosphorylation is required for DDA3's mitotic function.","method":"Mass spectrometry (phosphosite identification), phospho-mimicking and non-phosphorylatable mutants, siRNA rescue assay, immunofluorescence","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-identified site, mutagenesis rescue in cells, single lab","pmids":["20117088"],"is_preprint":false},{"year":2011,"finding":"DDA3 interacts with MCAK (a plus-end MT depolymerase) and localizes to kinetochores. DDA3 depletion causes CENP-E accumulation at kinetochores of unaligned chromosomes; Aurora B kinase activity and chromosomal passenger complex localization are unaffected by DDA3 depletion.","method":"Co-immunoprecipitation, immunofluorescence, siRNA depletion","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP and immunofluorescence, multiple readouts, single lab","pmids":["21426902"],"is_preprint":false},{"year":2011,"finding":"Mitotic kinases phosphorylate DDA3 at Ser22, Ser65, Ser70, and Ser223 (identified by mass spectrometry). Unphosphorylated DDA3 has both MT-polymerizing and MT-bundling activities; phospho-mimetic mutants at these sites lose both activities while retaining MT-binding. Cdk1 and Aurora A phosphorylation negatively regulate MT-polymerizing/bundling activities in vitro; Plk1 does not. Sequential phosphorylation by Aurora A and Plk1 inhibits phosphorylation by other kinases.","method":"Mass spectrometry (phosphosite identification), in vitro kinase assay, phospho-mimicking mutants, in vitro MT polymerization and bundling assays","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro kinase assay, mutagenesis, in vitro MT assays, multiple kinases tested, single lab","pmids":["21473853"],"is_preprint":false},{"year":2012,"finding":"DDA3 bundles and stabilizes microtubules in vivo and in vitro; overexpression increases acetylated and tyrosinated microtubule abundance. DDA3 overexpression suppresses neurite/axon outgrowth in PC12, N2a, and hippocampal neurons, while its depletion accelerates neurite/axon formation. DDA3 knockdown reduces β3-tubulin levels contributing to spontaneous neuritogenesis. DDA3 is downregulated during neuronal differentiation.","method":"Overexpression, siRNA knockdown, in vitro MT bundling/stabilization assays, immunofluorescence, PC12/N2a/hippocampal neuron cell culture, Western blot","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro MT assays plus multiple cell line models with both gain- and loss-of-function, orthogonal methods","pmids":["22467851"],"is_preprint":false},{"year":2013,"finding":"DDA3 interacts with EB1 via an SxIP motif in its C-terminal Pro/Ser-rich region, enabling MT plus-end loading and tracking in an EB1-dependent manner (shown by TIRF microscopy and time-lapse imaging). EB1-dependent loading of DDA3 stabilizes MT plus-ends at the cell cortex and facilitates directional cell migration. EB1 acetylation potentially regulates the DDA3–EB1 interaction and EGF-elicited cell migration.","method":"Biochemical interaction mapping, TIRF microscopy, time-lapse imaging, siRNA knockdown, EGF stimulation","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — TIRF + time-lapse imaging, SxIP motif identification, directional migration assay, single lab with multiple orthogonal methods","pmids":["23652583"],"is_preprint":false},{"year":2016,"finding":"ASB7 (a Cullin 5–SOCS box E3 ligase) ubiquitinates DDA3 and targets it for proteasomal degradation. Microtubule presence prevents the ASB7–DDA3 interaction, stabilizing DDA3. ASB7 knockdown increases DDA3 levels, increases Kif2a recruitment to the spindle, reduces MT polymerization, and causes unaligned chromosomes — a phenotype rescued by DDA3 deletion.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, genetic epistasis (double knockdown rescue), immunofluorescence","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — ubiquitination assay, epistasis rescue, MT-dependent interaction, multiple orthogonal methods","pmids":["27697924"],"is_preprint":false},{"year":2016,"finding":"Mdp3 (MAP7D3) forms a complex with DDA3 and inhibits DDA3-mediated Kif2a recruitment to the mitotic spindle. Mdp3 depletion leads to aberrant Kif2a activity at the MT minus end, decreased spindle stability, unaligned chromosomes, lagging chromosomes, and chromosome bridges. DDA3 and Mdp3 act oppositely on minus-end MT dynamics but do not affect each other's localization.","method":"Co-immunoprecipitation, siRNA knockdown, immunofluorescence, live imaging","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — co-IP establishing complex, siRNA epistasis, multiple mitotic phenotype readouts, orthogonal imaging","pmids":["27284004"],"is_preprint":false},{"year":2016,"finding":"ANKRD53 interacts with DDA3 (identified by proteomic analysis) and is recruited to the mitotic spindle by DDA3. ANKRD53 counteracts DDA3 activity for spindle MT polymerization. ANKRD53 depletion delays mitosis, increases unaligned chromosomes, decreases spindle MT polymerization, activates the spindle assembly checkpoint, and causes bi-nuclei and polylobed nuclei.","method":"Proteomic/MS analysis, co-immunoprecipitation, siRNA knockdown, immunofluorescence","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — MS identification, co-IP, siRNA phenotype readouts, single lab","pmids":["26820536"],"is_preprint":false},{"year":2016,"finding":"Ska1 is recruited to kinetochores by DDA3 to stabilize end-on kinetochore–MT attachment. After Kif2a is recruited to the spindle by DDA3, Ska1 targets Kif2a to the minus-end of spindle MTs to facilitate spindle dynamics. These interactions provide a molecular link between spindle dynamics and kinetochore composition.","method":"Co-immunoprecipitation, siRNA knockdown, immunofluorescence, rescue experiments","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP, siRNA epistasis, multiple readouts, single lab","pmids":["26797278"],"is_preprint":false},{"year":2018,"finding":"PSRC1 overexpression in macrophages reduces cellular cholesterol content, increases cholesterol efflux, and inhibits foam cell formation by upregulating PPARγ and LXRα expression. In apoE−/− mice, adenoviral PSRC1 overexpression inhibits atherosclerotic lesion development, decreases plasma TC/TG/LDL-C/inflammatory cytokines, and increases HDL-C. The β-catenin pathway (upstream of PPARγ and LXRα) is elevated in PSRC1-overexpressing liver and macrophages; NF-κB activity is decreased.","method":"Adenoviral overexpression in RAW264.7 cells and apoE−/− mice, cholesterol efflux assay, Western blot, ELISA, histology","journal":"Journal of molecular and cellular cardiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro and in vivo overexpression with multiple biochemical readouts, single lab","pmids":["29378206"],"is_preprint":false},{"year":2019,"finding":"c-Cbl acts as an E3 ubiquitin ligase that degrades DDA3. c-Cbl depletion increases DDA3 protein levels, leading to increased Kif2a recruitment to the spindle, reduced spindle formation, chromosome alignment defects, centrosome over-duplication, and centriole amplification.","method":"siRNA knockdown, Western blot, immunofluorescence, co-immunoprecipitation (implied by E3 ligase assay)","journal":"Molecules and cells","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — depletion-based epistasis with multiple phenotypic readouts, E3 ligase activity inferred, single lab","pmids":["31722512"],"is_preprint":false},{"year":2022,"finding":"PSRC1 deletion in macrophages impairs reverse cholesterol transport and enhances cholesterol uptake and inflammation. PSRC1 overexpression in macrophages overexpressing PSRC1 rescues proatherogenic phenotype in TMAO-stimulated cells, partly attributed to sulfotransferase 2B1b (SULT2B1b) inhibition. PSRC1 overexpression in vitro inhibited FMO3 expression, and this effect was rescued by an ERα inhibitor, indicating ERα-mediated regulation.","method":"PSRC1 knockout/overexpression in macrophages, reverse cholesterol transport assay, hepatic RNA-seq, ERα inhibitor rescue, in vitro overexpression","journal":"Journal of molecular and cellular cardiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro mechanistic experiments with specific pathway inhibitor rescue, KO and OE, single lab","pmids":["35690006"],"is_preprint":false},{"year":2022,"finding":"PSRC1 deletion enriches TMA-producing gut bacteria, enhances plasma TMAO and betaine production, upregulates hepatic FMO3 expression, and promotes a proinflammatory colonic phenotype. Fecal microbiota transplant from PSRC1-KO mice to apoE−/− recipients elevated TMAO, plaque lipid deposition, and macrophage accumulation. PSRC1 overexpression in vitro inhibits FMO3 via an ERα-dependent mechanism.","method":"PSRC1-KO mice, metagenomics, untargeted metabolomics, hepatic RNA-seq, fecal microbiota transplant, antibiotic treatment, in vitro overexpression with ERα inhibitor","journal":"Gut microbes","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO model with multi-omics, FMT causality test, in vitro mechanism, single lab with multiple methods","pmids":["35613310"],"is_preprint":false},{"year":2025,"finding":"PSRC1 is localized to spindle poles throughout all stages of mouse oocyte meiosis, co-localizing with spindle microtubules (confirmed by Taxol/nocodazole treatment). Psrc1 knockdown causes abnormal spindle morphology, sustained spindle assembly checkpoint activation, abnormal kinetochore–microtubule attachments, and increased aneuploidy. Both knockdown and overexpression of Psrc1 cause abnormal spindle assembly and increased large polar body rates.","method":"siRNA knockdown, mRNA overexpression, immunofluorescence, Taxol/nocodazole treatment, Western blot","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss- and gain-of-function in oocyte meiosis with multiple readouts, single study","pmids":["40810374"],"is_preprint":false}],"current_model":"PSRC1/DDA3 is a microtubule-associated protein that directly binds MTs via its C-terminal domain, recruits the MT depolymerase Kif2a to the mitotic spindle and spindle poles to control spindle MT dynamics (destabilization/poleward flux), and interacts with EB1/EB3, MCAK, Ska1, Mdp3, and ASPP2; its activity is regulated by phosphorylation (Cdk1, Aurora A, Plk1) and by ubiquitin-mediated degradation (ASB7, c-Cbl E3 ligases), and it is transcriptionally regulated by p53/p73 while also promoting β-catenin signaling and playing roles in directional cell migration, neuritogenesis, and macrophage cholesterol homeostasis."},"narrative":{"mechanistic_narrative":"PSRC1/DDA3 is a microtubule-associated protein that governs spindle microtubule dynamics during mitosis by acting as a recruitment platform for microtubule depolymerases [PMID:18411309]. It binds microtubules directly through its C-terminal domain, which both associates with the mitotic spindle and confers intrinsic microtubule-polymerizing and -bundling activity, whereas the N-terminal domain is dispensable for MT binding but required for proper spindle targeting [PMID:19738423, PMID:21473853]. Through this scaffold, PSRC1 recruits the depolymerase Kif2a to the spindle and spindle poles in a microtubule-dependent manner, and its loss produces unaligned chromosomes, reduced inter-kinetochore tension, slowed anaphase chromosome movement, and stabilized spindle microtubules, phenocopying Kif2a depletion [PMID:18411309]. PSRC1 coordinates a network of spindle and kinetochore factors: it tracks growing MT plus-ends via an SxIP-motif interaction with EB1 (and binds EB3) to stabilize plus-ends at the cortex and drive directional cell migration [PMID:17310996, PMID:23652583], engages the depolymerase MCAK and localizes to kinetochores [PMID:21426902], and links spindle dynamics to kinetochore composition by recruiting Ska1, which in turn targets Kif2a to MT minus-ends [PMID:26797278]. This activity is tightly controlled by mitotic phosphorylation — Cdk1 and Aurora A phosphorylate PSRC1 to suppress its MT-polymerizing/bundling activities, Ser225 phosphorylation is required for its mitotic function [PMID:20117088, PMID:21473853] — and by ubiquitin-mediated degradation through the ASB7 (Cullin5–SOCS box) and c-Cbl E3 ligases, with microtubules protecting PSRC1 from ASB7-driven turnover [PMID:27697924, PMID:31722512]. Antagonistic partners Mdp3 (MAP7D3) and ANKRD53 oppose PSRC1-dependent Kif2a recruitment and spindle MT polymerization, fine-tuning the balance [PMID:27284004, PMID:26820536]. Beyond mitosis, PSRC1 bundles and stabilizes microtubules to restrain neurite/axon outgrowth and is downregulated during neuronal differentiation [PMID:22467851], and it is required for normal spindle assembly and chromosome segregation in oocyte meiosis [PMID:40810374]. PSRC1 is embedded in p53 signaling as a direct transcriptional target — induced by p53/p73 in mouse but repressed by p53 in human cells — and modulates p53 output by inhibiting ASPP2-stimulated BAX activation and by promoting β-catenin–dependent transactivation of cyclin D1 [PMID:12082536, PMID:17310996, PMID:18291097, PMID:18793611]. Independently, PSRC1 promotes macrophage cholesterol efflux and reverse cholesterol transport and suppresses atherosclerosis, acting through β-catenin/PPARγ/LXRα and ERα-dependent control of hepatic FMO3 and the gut-microbiota–TMAO axis [PMID:29378206, PMID:35690006, PMID:35613310].","teleology":[{"year":1999,"claim":"Established PSRC1/DDA3 as a p53-responsive gene, framing its initial biological context within tumor-suppressor signaling and growth control.","evidence":"Differential mRNA display with actinomycin D/cycloheximide and colony-formation assay in H1299 cells","pmids":["10618717"],"confidence":"Medium","gaps":["Did not identify the gene product's molecular function","Mechanism of growth suppression undefined"]},{"year":2002,"claim":"Defined DDA3 as a direct transcriptional target of both p53 and p73 via a mapped response element, establishing the transcriptional wiring upstream of the protein.","evidence":"Luciferase reporter, EMSA, and p53-knockout MEFs in mouse","pmids":["12082536"],"confidence":"High","gaps":["Species-specific direction of regulation not yet recognized","No link to protein function"]},{"year":2007,"claim":"Identified DDA3 as a microtubule-associated protein binding EB3 and APC2, and tied it to β-catenin signaling, revealing its cytoskeletal and oncogenic activities.","evidence":"Yeast two-hybrid, GST pull-down, co-IP, in vitro MT binding, reporter assays, siRNA","pmids":["17310996"],"confidence":"High","gaps":["Mitotic role not yet established","Mechanism linking MT binding to β-catenin output unclear"]},{"year":2008,"claim":"Resolved that human DDA3 is repressed (not induced) by p53, exposing a species divergence in transcriptional control.","evidence":"ChIP, luciferase reporter, Western blot, RT-PCR in DNA-damaged human cells","pmids":["18291097"],"confidence":"High","gaps":["Functional consequence of repression for the protein's mitotic role not addressed"]},{"year":2008,"claim":"Defined DDA3's core mitotic mechanism — recruiting the depolymerase Kif2a to the spindle to control MT dynamics and chromosome segregation.","evidence":"Mass spectrometry co-purification, siRNA, live imaging, FRAP, Kif2a-knockdown phenocopy","pmids":["18411309"],"confidence":"High","gaps":["How DDA3 itself is targeted to poles not fully resolved","Regulation of recruitment timing unknown"]},{"year":2008,"claim":"Connected DDA3's MT function back to p53 signaling by showing it inhibits ASPP2-stimulated p53-mediated BAX transactivation.","evidence":"Yeast two-hybrid, GST pull-down, colocalization, luciferase reporter","pmids":["18793611"],"confidence":"Medium","gaps":["Single-lab interaction without reciprocal in vivo validation","Physiological relevance to apoptosis untested"]},{"year":2009,"claim":"Dissected the domain architecture, assigning MT binding/spindle association to the C-terminus and a regulatory/targeting role to the N-terminus.","evidence":"In vitro MT-binding, dominant-negative overexpression, immunofluorescence, live imaging","pmids":["19738423"],"confidence":"Medium","gaps":["No high-resolution structure of MT-binding region","Single lab"]},{"year":2010,"claim":"Identified Ser225 mitotic phosphorylation as functionally required, introducing phospho-regulation as a control layer on DDA3's mitotic activity.","evidence":"MS phosphosite mapping, phospho-mimic/non-phosphorylatable mutants, siRNA rescue","pmids":["20117088"],"confidence":"Medium","gaps":["Responsible kinase not identified here","Single lab"]},{"year":2011,"claim":"Mapped a multi-site phosphocode and assigned Cdk1 and Aurora A as negative regulators of DDA3's intrinsic MT-polymerizing/bundling activities.","evidence":"MS phosphosite mapping, in vitro kinase and MT polymerization/bundling assays, phospho-mimic mutants","pmids":["21473853"],"confidence":"High","gaps":["In vivo confirmation of site-specific kinase action limited","Plk1 role negative but its function on DDA3 unclear"]},{"year":2011,"claim":"Extended DDA3's interactome to MCAK and kinetochores, linking it to CENP-E clearance from unaligned chromosomes.","evidence":"Co-IP, immunofluorescence, siRNA depletion","pmids":["21426902"],"confidence":"Medium","gaps":["Co-IP without reciprocal validation","Direct MCAK binding region not mapped"]},{"year":2012,"claim":"Established a non-mitotic role: DDA3 bundles/stabilizes microtubules to suppress neurite and axon outgrowth, with downregulation enabling differentiation.","evidence":"Gain/loss-of-function in PC12, N2a, hippocampal neurons; in vitro MT assays; Western blot","pmids":["22467851"],"confidence":"High","gaps":["Upstream signals controlling DDA3 in neurons unknown","Relation to phospho-regulation untested in neurons"]},{"year":2013,"claim":"Defined the SxIP-motif EB1 interaction that loads DDA3 onto growing MT plus-ends, linking plus-end tracking to cortical MT stabilization and directional migration.","evidence":"Interaction mapping, TIRF and time-lapse imaging, siRNA, EGF stimulation","pmids":["23652583"],"confidence":"High","gaps":["Role of EB1 acetylation in vivo not fully resolved","Integration with mitotic functions unclear"]},{"year":2016,"claim":"Identified two E3 ligases (ASB7, c-Cbl) and MT-protective stabilization controlling DDA3 abundance, establishing degradation as a key regulator of Kif2a recruitment and spindle integrity.","evidence":"Ubiquitination assays, co-IP, siRNA, epistasis rescue, immunofluorescence","pmids":["27697924","31722512"],"confidence":"High","gaps":["c-Cbl E3 activity on DDA3 inferred rather than directly assayed","Cell-cycle timing of degradation not fully resolved"]},{"year":2016,"claim":"Revealed antagonistic regulators (Mdp3/MAP7D3, ANKRD53) and the Ska1 link, building a balanced network that tunes DDA3-dependent Kif2a recruitment and minus-end dynamics.","evidence":"Co-IP, MS/proteomics, siRNA epistasis, immunofluorescence, live imaging, rescue","pmids":["27284004","26820536","26797278"],"confidence":"Medium","gaps":["Direct binding interfaces not mapped for all partners","Single-lab co-IP for several interactions"]},{"year":2018,"claim":"Opened a metabolic axis: PSRC1 promotes macrophage cholesterol efflux and suppresses atherosclerosis via β-catenin/PPARγ/LXRα activation.","evidence":"Adenoviral overexpression in RAW264.7 and apoE−/− mice, cholesterol efflux assay, Western blot, ELISA, histology","pmids":["29378206"],"confidence":"Medium","gaps":["Mechanistic link between MT function and lipid metabolism unestablished","Overexpression-based, single lab"]},{"year":2022,"claim":"Established loss-of-function PSRC1 phenotypes in cholesterol homeostasis, implicating ERα-dependent FMO3 regulation and the gut-microbiota–TMAO axis in its anti-atherosclerotic role.","evidence":"PSRC1-KO/OE macrophages and mice, reverse cholesterol transport, multi-omics, FMT, ERα inhibitor rescue","pmids":["35690006","35613310"],"confidence":"Medium","gaps":["Direct molecular target of PSRC1 in this pathway unknown","Connection to the cytoskeletal function unresolved"]},{"year":2025,"claim":"Extended the spindle function to meiosis, showing PSRC1 is required for normal oocyte spindle assembly, kinetochore–MT attachment, and euploidy.","evidence":"siRNA knockdown, mRNA overexpression, immunofluorescence, Taxol/nocodazole, Western blot in mouse oocytes","pmids":["40810374"],"confidence":"Medium","gaps":["Whether meiotic role uses the same Kif2a/EB1 machinery not tested","Single study"]},{"year":null,"claim":"How PSRC1's microtubule-scaffolding function mechanistically connects to its metabolic and transcriptional roles, and whether a structural basis exists for its MT and partner binding, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of PSRC1 or its MT/EB1/Kif2a interfaces","No unified mechanism linking spindle and cholesterol functions","Human disease causation not directly demonstrated in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[2,4,6,9,10,11]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,11,15]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[4,5,13,14]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[9,10]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[2,4,6,10,11]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[4,6,20]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3,5]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[4,8,12,13,14,15,17]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,3]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[16,18,19]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,16]}],"complexes":[],"partners":["KIF2A","EB1 (MAPRE1)","EB3 (MAPRE3)","MCAK (KIF2C)","SKA1","MAP7D3","ANKRD53","ASPP2 (TP53BP2)"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6PGN9","full_name":"Proline/serine-rich coiled-coil protein 1","aliases":[],"length_aa":363,"mass_kda":38.8,"function":"Required for normal progression through mitosis. Required for normal congress of chromosomes at the metaphase plate, and for normal rate of chromosomal segregation during anaphase. Plays a role in the regulation of mitotic spindle dynamics. Increases the rate of turnover of microtubules on metaphase spindles, and contributes to the generation of normal tension across sister kinetochores. Recruits KIF2A and ANKRD53 to the mitotic spindle and spindle poles. May participate in p53/TP53-regulated growth suppression","subcellular_location":"Cytoplasm; Cytoplasm, cytoskeleton, spindle; Cytoplasm, cytoskeleton, spindle pole","url":"https://www.uniprot.org/uniprotkb/Q6PGN9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PSRC1","classification":"Not Classified","n_dependent_lines":94,"n_total_lines":1208,"dependency_fraction":0.07781456953642384},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PSRC1","total_profiled":1310},"omim":[{"mim_id":"617009","title":"ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 53; ANKRD53","url":"https://www.omim.org/entry/617009"},{"mim_id":"613589","title":"LOW DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 6; LDLCQ6","url":"https://www.omim.org/entry/613589"},{"mim_id":"613126","title":"PROLINE/SERINE-RICH COILED-COIL PROTEIN 1; PSRC1","url":"https://www.omim.org/entry/613126"},{"mim_id":"602458","title":"SORTILIN; SORT1","url":"https://www.omim.org/entry/602458"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":91.4},{"tissue":"retina","ntpm":38.7}],"url":"https://www.proteinatlas.org/search/PSRC1"},"hgnc":{"alias_symbol":["DDA3"],"prev_symbol":[]},"alphafold":{"accession":"Q6PGN9","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6PGN9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6PGN9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6PGN9-F1-predicted_aligned_error_v6.png","plddt_mean":57.41},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PSRC1","jax_strain_url":"https://www.jax.org/strain/search?query=PSRC1"},"sequence":{"accession":"Q6PGN9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6PGN9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6PGN9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6PGN9"}},"corpus_meta":[{"pmid":"18649068","id":"PMC_18649068","title":"The novel genetic variant predisposing to coronary artery disease in the region of the PSRC1 and CELSR2 genes on chromosome 1 associates with serum cholesterol.","date":"2008","source":"Journal of molecular medicine (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/18649068","citation_count":76,"is_preprint":false},{"pmid":"18411309","id":"PMC_18411309","title":"DDA3 recruits microtubule depolymerase Kif2a to spindle poles and controls spindle dynamics and mitotic chromosome movement.","date":"2008","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/18411309","citation_count":68,"is_preprint":false},{"pmid":"17310996","id":"PMC_17310996","title":"p53 downstream target DDA3 is a novel microtubule-associated protein that interacts with end-binding protein EB3 and activates beta-catenin pathway.","date":"2007","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/17310996","citation_count":44,"is_preprint":false},{"pmid":"35613310","id":"PMC_35613310","title":"Deficiency of PSRC1 accelerates atherosclerosis by increasing TMAO 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CELSR2/PSRC1/SORT1 Cluster That Associates With LDL-C and Resting Metabolic Rate.","date":"2025","source":"The Journal of clinical endocrinology and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/39018443","citation_count":2,"is_preprint":false},{"pmid":"40194605","id":"PMC_40194605","title":"Phosphocreatine alleviates monocrotaline-induced liver injury dependent on PSRC1-regulated endoplasmic reticulum stress.","date":"2025","source":"Biochemical pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/40194605","citation_count":1,"is_preprint":false},{"pmid":"38028723","id":"PMC_38028723","title":"Polymorphism of rs599839 in the PSRC1 gene is associated with coronary artery disease in an Iranian population.","date":"2023","source":"Journal of cardiovascular and thoracic research","url":"https://pubmed.ncbi.nlm.nih.gov/38028723","citation_count":0,"is_preprint":false},{"pmid":"42019808","id":"PMC_42019808","title":"Causal statistical association between remnant cholesterol and coronary heart disease: genetic insights into the PSRC1-CELSR2-SORT1 gene cluster.","date":"2026","source":"Journal of lipid research","url":"https://pubmed.ncbi.nlm.nih.gov/42019808","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.11.26.625550","title":"Transcriptome of the murine duodenum during recovery after a lethal dose of total body irradiation","date":"2024-11-27","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.26.625550","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.30.662294","title":"Multi-Tissue Profiling Reveals tissue-specific protein regulation and relationships Between Protein Quantitative Trait Loci (pQTLs) and Cardiometabolic Disease","date":"2025-07-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.30.662294","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19252,"output_tokens":5605,"usd":0.070916,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":14221,"output_tokens":5282,"usd":0.101578,"stage2_stop_reason":"end_turn"},"total_usd":0.172494,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"DDA3 (PSRC1) was identified as a p53-regulated gene: DDA3 mRNA is transcriptionally induced by p53 in a cycloheximide-insensitive, actinomycin D-sensitive manner, indicating direct transcriptional activation without requiring de novo protein synthesis. Overexpression of DDA3 suppressed colony formation in H1299 lung carcinoma cells.\",\n      \"method\": \"Differential mRNA display, actinomycin D/cycloheximide treatment, colony formation assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — transcriptional regulation demonstrated by pharmacological inhibitors and overexpression, single lab with two orthogonal methods\",\n      \"pmids\": [\"10618717\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Mouse DDA3 is a direct transcriptional target of both p53 and p73: a p53 response element (RE2) in the DDA3 gene was shown by luciferase reporter assay and gel mobility shift analysis to bind wild-type p53 and confer transactivation. DDA3 induction by DNA damage was absent in p53-knockout MEFs. p73 family members also transactivated DDA3 via RE2.\",\n      \"method\": \"Luciferase reporter assay, gel mobility shift assay, p53-knockout MEFs, overexpression\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (reporter assay, EMSA, KO cells) in single lab, replicated across p53 and p73\",\n      \"pmids\": [\"12082536\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"DDA3 is a microtubule-associated protein that interacts with plus-end binding protein EB3. Interaction was confirmed by GST pull-down and co-immunoprecipitation (requiring intact microtubules). Interaction domains were mapped to DDA3 aa 118–241 and 242–329 (EB3 binding and MT-bundling) and EB3 N- and C-termini. DDA3 directly binds microtubules in vitro and cooperates with EB3 for MT binding. DDA3 also interacts with APC2. Ectopic expression of DDA3 and EB3 enhanced beta-catenin-dependent transactivation and cyclin D1; knockdown inhibited beta-catenin signaling and colony formation.\",\n      \"method\": \"Yeast two-hybrid, GST pull-down, co-immunoprecipitation, in vitro microtubule-binding assay, immunofluorescence, reporter assay, siRNA knockdown\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal biochemical methods (Y2H, GST pulldown, co-IP, in vitro MT binding, reporter), domain mapping, functional rescue\",\n      \"pmids\": [\"17310996\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human DDA3 is transcriptionally repressed by p53 (opposite to mouse DDA3): p53 binds three consensus El-Deiry decamers at −1478/−1403 of the hDDA3 promoter as shown by chromatin immunoprecipitation, and luciferase analysis showed this region mediates p53-dependent repression. hDDA3 mRNA and protein are suppressed in DNA-damaged cells in a wild-type p53-dependent manner.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), luciferase reporter assay, Western blot, real-time PCR\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — ChIP plus reporter assay with mutant p53 controls, multiple orthogonal methods in single study\",\n      \"pmids\": [\"18291097\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"DDA3 recruits microtubule depolymerase Kif2a to the mitotic spindle and spindle poles in a microtubule-dependent manner. DDA3 depletion causes unaligned chromosomes, reduced inter-kinetochore tension, decreased anaphase chromosome velocity, increased spindle MT steady-state levels, reduced MT turnover, and increased MT polymerization rate — phenocopying partial Kif2a knockdown.\",\n      \"method\": \"siRNA depletion, mass spectrometry (co-purification), immunofluorescence, live imaging, fluorescence recovery after photobleaching (FRAP)\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — co-purification by MS, siRNA with multiple quantitative readouts (tension, velocity, FRAP), phenocopy experiment with Kif2a KD, replicated in multiple assays\",\n      \"pmids\": [\"18411309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"DDA3 interacts with ASPP2 (a p53-binding protein). The interaction domain on DDA3 maps to aa 118–241; both N- and C-terminal regions of ASPP2 bind DDA3. DDA3 dose-dependently inhibits ASPP2-stimulated p53-mediated BAX promoter activation without interfering with ASPP2–p53 binding.\",\n      \"method\": \"Yeast two-hybrid screening, GST pull-down, immunofluorescence colocalization, luciferase reporter assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — GST pulldown + reporter assay, domain mapping, single lab\",\n      \"pmids\": [\"18793611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Domain analysis of DDA3: the C-terminal domain directly binds microtubules in vitro and associates with the mitotic spindle in vivo; the N-terminal domain does not bind MTs but acts dominant-negatively, preventing endogenous DDA3 spindle association and reducing spindle-associated Kif2a while increasing spindle MT density.\",\n      \"method\": \"In vitro microtubule-binding assay, dominant-negative overexpression, immunofluorescence, live imaging\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro MT binding, dominant-negative dissection, single lab with multiple readouts\",\n      \"pmids\": [\"19738423\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"DDA3 is phosphorylated on Ser225 during mitosis. The phospho-mimicking S225D variant rescues DDA3-knockdown mitotic defects (unaligned chromosomes), whereas the non-phosphorylatable S225A mutant does not, demonstrating that Ser225 phosphorylation is required for DDA3's mitotic function.\",\n      \"method\": \"Mass spectrometry (phosphosite identification), phospho-mimicking and non-phosphorylatable mutants, siRNA rescue assay, immunofluorescence\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-identified site, mutagenesis rescue in cells, single lab\",\n      \"pmids\": [\"20117088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"DDA3 interacts with MCAK (a plus-end MT depolymerase) and localizes to kinetochores. DDA3 depletion causes CENP-E accumulation at kinetochores of unaligned chromosomes; Aurora B kinase activity and chromosomal passenger complex localization are unaffected by DDA3 depletion.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, siRNA depletion\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP and immunofluorescence, multiple readouts, single lab\",\n      \"pmids\": [\"21426902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Mitotic kinases phosphorylate DDA3 at Ser22, Ser65, Ser70, and Ser223 (identified by mass spectrometry). Unphosphorylated DDA3 has both MT-polymerizing and MT-bundling activities; phospho-mimetic mutants at these sites lose both activities while retaining MT-binding. Cdk1 and Aurora A phosphorylation negatively regulate MT-polymerizing/bundling activities in vitro; Plk1 does not. Sequential phosphorylation by Aurora A and Plk1 inhibits phosphorylation by other kinases.\",\n      \"method\": \"Mass spectrometry (phosphosite identification), in vitro kinase assay, phospho-mimicking mutants, in vitro MT polymerization and bundling assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro kinase assay, mutagenesis, in vitro MT assays, multiple kinases tested, single lab\",\n      \"pmids\": [\"21473853\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"DDA3 bundles and stabilizes microtubules in vivo and in vitro; overexpression increases acetylated and tyrosinated microtubule abundance. DDA3 overexpression suppresses neurite/axon outgrowth in PC12, N2a, and hippocampal neurons, while its depletion accelerates neurite/axon formation. DDA3 knockdown reduces β3-tubulin levels contributing to spontaneous neuritogenesis. DDA3 is downregulated during neuronal differentiation.\",\n      \"method\": \"Overexpression, siRNA knockdown, in vitro MT bundling/stabilization assays, immunofluorescence, PC12/N2a/hippocampal neuron cell culture, Western blot\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro MT assays plus multiple cell line models with both gain- and loss-of-function, orthogonal methods\",\n      \"pmids\": [\"22467851\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DDA3 interacts with EB1 via an SxIP motif in its C-terminal Pro/Ser-rich region, enabling MT plus-end loading and tracking in an EB1-dependent manner (shown by TIRF microscopy and time-lapse imaging). EB1-dependent loading of DDA3 stabilizes MT plus-ends at the cell cortex and facilitates directional cell migration. EB1 acetylation potentially regulates the DDA3–EB1 interaction and EGF-elicited cell migration.\",\n      \"method\": \"Biochemical interaction mapping, TIRF microscopy, time-lapse imaging, siRNA knockdown, EGF stimulation\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — TIRF + time-lapse imaging, SxIP motif identification, directional migration assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"23652583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"ASB7 (a Cullin 5–SOCS box E3 ligase) ubiquitinates DDA3 and targets it for proteasomal degradation. Microtubule presence prevents the ASB7–DDA3 interaction, stabilizing DDA3. ASB7 knockdown increases DDA3 levels, increases Kif2a recruitment to the spindle, reduces MT polymerization, and causes unaligned chromosomes — a phenotype rescued by DDA3 deletion.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, genetic epistasis (double knockdown rescue), immunofluorescence\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ubiquitination assay, epistasis rescue, MT-dependent interaction, multiple orthogonal methods\",\n      \"pmids\": [\"27697924\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Mdp3 (MAP7D3) forms a complex with DDA3 and inhibits DDA3-mediated Kif2a recruitment to the mitotic spindle. Mdp3 depletion leads to aberrant Kif2a activity at the MT minus end, decreased spindle stability, unaligned chromosomes, lagging chromosomes, and chromosome bridges. DDA3 and Mdp3 act oppositely on minus-end MT dynamics but do not affect each other's localization.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, immunofluorescence, live imaging\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — co-IP establishing complex, siRNA epistasis, multiple mitotic phenotype readouts, orthogonal imaging\",\n      \"pmids\": [\"27284004\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"ANKRD53 interacts with DDA3 (identified by proteomic analysis) and is recruited to the mitotic spindle by DDA3. ANKRD53 counteracts DDA3 activity for spindle MT polymerization. ANKRD53 depletion delays mitosis, increases unaligned chromosomes, decreases spindle MT polymerization, activates the spindle assembly checkpoint, and causes bi-nuclei and polylobed nuclei.\",\n      \"method\": \"Proteomic/MS analysis, co-immunoprecipitation, siRNA knockdown, immunofluorescence\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — MS identification, co-IP, siRNA phenotype readouts, single lab\",\n      \"pmids\": [\"26820536\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Ska1 is recruited to kinetochores by DDA3 to stabilize end-on kinetochore–MT attachment. After Kif2a is recruited to the spindle by DDA3, Ska1 targets Kif2a to the minus-end of spindle MTs to facilitate spindle dynamics. These interactions provide a molecular link between spindle dynamics and kinetochore composition.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, immunofluorescence, rescue experiments\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP, siRNA epistasis, multiple readouts, single lab\",\n      \"pmids\": [\"26797278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PSRC1 overexpression in macrophages reduces cellular cholesterol content, increases cholesterol efflux, and inhibits foam cell formation by upregulating PPARγ and LXRα expression. In apoE−/− mice, adenoviral PSRC1 overexpression inhibits atherosclerotic lesion development, decreases plasma TC/TG/LDL-C/inflammatory cytokines, and increases HDL-C. The β-catenin pathway (upstream of PPARγ and LXRα) is elevated in PSRC1-overexpressing liver and macrophages; NF-κB activity is decreased.\",\n      \"method\": \"Adenoviral overexpression in RAW264.7 cells and apoE−/− mice, cholesterol efflux assay, Western blot, ELISA, histology\",\n      \"journal\": \"Journal of molecular and cellular cardiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro and in vivo overexpression with multiple biochemical readouts, single lab\",\n      \"pmids\": [\"29378206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"c-Cbl acts as an E3 ubiquitin ligase that degrades DDA3. c-Cbl depletion increases DDA3 protein levels, leading to increased Kif2a recruitment to the spindle, reduced spindle formation, chromosome alignment defects, centrosome over-duplication, and centriole amplification.\",\n      \"method\": \"siRNA knockdown, Western blot, immunofluorescence, co-immunoprecipitation (implied by E3 ligase assay)\",\n      \"journal\": \"Molecules and cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — depletion-based epistasis with multiple phenotypic readouts, E3 ligase activity inferred, single lab\",\n      \"pmids\": [\"31722512\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PSRC1 deletion in macrophages impairs reverse cholesterol transport and enhances cholesterol uptake and inflammation. PSRC1 overexpression in macrophages overexpressing PSRC1 rescues proatherogenic phenotype in TMAO-stimulated cells, partly attributed to sulfotransferase 2B1b (SULT2B1b) inhibition. PSRC1 overexpression in vitro inhibited FMO3 expression, and this effect was rescued by an ERα inhibitor, indicating ERα-mediated regulation.\",\n      \"method\": \"PSRC1 knockout/overexpression in macrophages, reverse cholesterol transport assay, hepatic RNA-seq, ERα inhibitor rescue, in vitro overexpression\",\n      \"journal\": \"Journal of molecular and cellular cardiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro mechanistic experiments with specific pathway inhibitor rescue, KO and OE, single lab\",\n      \"pmids\": [\"35690006\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PSRC1 deletion enriches TMA-producing gut bacteria, enhances plasma TMAO and betaine production, upregulates hepatic FMO3 expression, and promotes a proinflammatory colonic phenotype. Fecal microbiota transplant from PSRC1-KO mice to apoE−/− recipients elevated TMAO, plaque lipid deposition, and macrophage accumulation. PSRC1 overexpression in vitro inhibits FMO3 via an ERα-dependent mechanism.\",\n      \"method\": \"PSRC1-KO mice, metagenomics, untargeted metabolomics, hepatic RNA-seq, fecal microbiota transplant, antibiotic treatment, in vitro overexpression with ERα inhibitor\",\n      \"journal\": \"Gut microbes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO model with multi-omics, FMT causality test, in vitro mechanism, single lab with multiple methods\",\n      \"pmids\": [\"35613310\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PSRC1 is localized to spindle poles throughout all stages of mouse oocyte meiosis, co-localizing with spindle microtubules (confirmed by Taxol/nocodazole treatment). Psrc1 knockdown causes abnormal spindle morphology, sustained spindle assembly checkpoint activation, abnormal kinetochore–microtubule attachments, and increased aneuploidy. Both knockdown and overexpression of Psrc1 cause abnormal spindle assembly and increased large polar body rates.\",\n      \"method\": \"siRNA knockdown, mRNA overexpression, immunofluorescence, Taxol/nocodazole treatment, Western blot\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss- and gain-of-function in oocyte meiosis with multiple readouts, single study\",\n      \"pmids\": [\"40810374\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PSRC1/DDA3 is a microtubule-associated protein that directly binds MTs via its C-terminal domain, recruits the MT depolymerase Kif2a to the mitotic spindle and spindle poles to control spindle MT dynamics (destabilization/poleward flux), and interacts with EB1/EB3, MCAK, Ska1, Mdp3, and ASPP2; its activity is regulated by phosphorylation (Cdk1, Aurora A, Plk1) and by ubiquitin-mediated degradation (ASB7, c-Cbl E3 ligases), and it is transcriptionally regulated by p53/p73 while also promoting β-catenin signaling and playing roles in directional cell migration, neuritogenesis, and macrophage cholesterol homeostasis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PSRC1/DDA3 is a microtubule-associated protein that governs spindle microtubule dynamics during mitosis by acting as a recruitment platform for microtubule depolymerases [#4]. It binds microtubules directly through its C-terminal domain, which both associates with the mitotic spindle and confers intrinsic microtubule-polymerizing and -bundling activity, whereas the N-terminal domain is dispensable for MT binding but required for proper spindle targeting [#6, #9]. Through this scaffold, PSRC1 recruits the depolymerase Kif2a to the spindle and spindle poles in a microtubule-dependent manner, and its loss produces unaligned chromosomes, reduced inter-kinetochore tension, slowed anaphase chromosome movement, and stabilized spindle microtubules, phenocopying Kif2a depletion [#4]. PSRC1 coordinates a network of spindle and kinetochore factors: it tracks growing MT plus-ends via an SxIP-motif interaction with EB1 (and binds EB3) to stabilize plus-ends at the cortex and drive directional cell migration [#2, #11], engages the depolymerase MCAK and localizes to kinetochores [#8], and links spindle dynamics to kinetochore composition by recruiting Ska1, which in turn targets Kif2a to MT minus-ends [#15]. This activity is tightly controlled by mitotic phosphorylation — Cdk1 and Aurora A phosphorylate PSRC1 to suppress its MT-polymerizing/bundling activities, Ser225 phosphorylation is required for its mitotic function [#7, #9] — and by ubiquitin-mediated degradation through the ASB7 (Cullin5–SOCS box) and c-Cbl E3 ligases, with microtubules protecting PSRC1 from ASB7-driven turnover [#12, #17]. Antagonistic partners Mdp3 (MAP7D3) and ANKRD53 oppose PSRC1-dependent Kif2a recruitment and spindle MT polymerization, fine-tuning the balance [#13, #14]. Beyond mitosis, PSRC1 bundles and stabilizes microtubules to restrain neurite/axon outgrowth and is downregulated during neuronal differentiation [#10], and it is required for normal spindle assembly and chromosome segregation in oocyte meiosis [#20]. PSRC1 is embedded in p53 signaling as a direct transcriptional target — induced by p53/p73 in mouse but repressed by p53 in human cells — and modulates p53 output by inhibiting ASPP2-stimulated BAX activation and by promoting β-catenin–dependent transactivation of cyclin D1 [#1, #2, #3, #5]. Independently, PSRC1 promotes macrophage cholesterol efflux and reverse cholesterol transport and suppresses atherosclerosis, acting through β-catenin/PPARγ/LXRα and ERα-dependent control of hepatic FMO3 and the gut-microbiota–TMAO axis [#16, #18, #19].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established PSRC1/DDA3 as a p53-responsive gene, framing its initial biological context within tumor-suppressor signaling and growth control.\",\n      \"evidence\": \"Differential mRNA display with actinomycin D/cycloheximide and colony-formation assay in H1299 cells\",\n      \"pmids\": [\"10618717\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not identify the gene product's molecular function\", \"Mechanism of growth suppression undefined\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Defined DDA3 as a direct transcriptional target of both p53 and p73 via a mapped response element, establishing the transcriptional wiring upstream of the protein.\",\n      \"evidence\": \"Luciferase reporter, EMSA, and p53-knockout MEFs in mouse\",\n      \"pmids\": [\"12082536\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Species-specific direction of regulation not yet recognized\", \"No link to protein function\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identified DDA3 as a microtubule-associated protein binding EB3 and APC2, and tied it to β-catenin signaling, revealing its cytoskeletal and oncogenic activities.\",\n      \"evidence\": \"Yeast two-hybrid, GST pull-down, co-IP, in vitro MT binding, reporter assays, siRNA\",\n      \"pmids\": [\"17310996\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mitotic role not yet established\", \"Mechanism linking MT binding to β-catenin output unclear\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Resolved that human DDA3 is repressed (not induced) by p53, exposing a species divergence in transcriptional control.\",\n      \"evidence\": \"ChIP, luciferase reporter, Western blot, RT-PCR in DNA-damaged human cells\",\n      \"pmids\": [\"18291097\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of repression for the protein's mitotic role not addressed\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defined DDA3's core mitotic mechanism — recruiting the depolymerase Kif2a to the spindle to control MT dynamics and chromosome segregation.\",\n      \"evidence\": \"Mass spectrometry co-purification, siRNA, live imaging, FRAP, Kif2a-knockdown phenocopy\",\n      \"pmids\": [\"18411309\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How DDA3 itself is targeted to poles not fully resolved\", \"Regulation of recruitment timing unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Connected DDA3's MT function back to p53 signaling by showing it inhibits ASPP2-stimulated p53-mediated BAX transactivation.\",\n      \"evidence\": \"Yeast two-hybrid, GST pull-down, colocalization, luciferase reporter\",\n      \"pmids\": [\"18793611\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab interaction without reciprocal in vivo validation\", \"Physiological relevance to apoptosis untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Dissected the domain architecture, assigning MT binding/spindle association to the C-terminus and a regulatory/targeting role to the N-terminus.\",\n      \"evidence\": \"In vitro MT-binding, dominant-negative overexpression, immunofluorescence, live imaging\",\n      \"pmids\": [\"19738423\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No high-resolution structure of MT-binding region\", \"Single lab\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified Ser225 mitotic phosphorylation as functionally required, introducing phospho-regulation as a control layer on DDA3's mitotic activity.\",\n      \"evidence\": \"MS phosphosite mapping, phospho-mimic/non-phosphorylatable mutants, siRNA rescue\",\n      \"pmids\": [\"20117088\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Responsible kinase not identified here\", \"Single lab\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Mapped a multi-site phosphocode and assigned Cdk1 and Aurora A as negative regulators of DDA3's intrinsic MT-polymerizing/bundling activities.\",\n      \"evidence\": \"MS phosphosite mapping, in vitro kinase and MT polymerization/bundling assays, phospho-mimic mutants\",\n      \"pmids\": [\"21473853\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo confirmation of site-specific kinase action limited\", \"Plk1 role negative but its function on DDA3 unclear\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Extended DDA3's interactome to MCAK and kinetochores, linking it to CENP-E clearance from unaligned chromosomes.\",\n      \"evidence\": \"Co-IP, immunofluorescence, siRNA depletion\",\n      \"pmids\": [\"21426902\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Co-IP without reciprocal validation\", \"Direct MCAK binding region not mapped\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Established a non-mitotic role: DDA3 bundles/stabilizes microtubules to suppress neurite and axon outgrowth, with downregulation enabling differentiation.\",\n      \"evidence\": \"Gain/loss-of-function in PC12, N2a, hippocampal neurons; in vitro MT assays; Western blot\",\n      \"pmids\": [\"22467851\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Upstream signals controlling DDA3 in neurons unknown\", \"Relation to phospho-regulation untested in neurons\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined the SxIP-motif EB1 interaction that loads DDA3 onto growing MT plus-ends, linking plus-end tracking to cortical MT stabilization and directional migration.\",\n      \"evidence\": \"Interaction mapping, TIRF and time-lapse imaging, siRNA, EGF stimulation\",\n      \"pmids\": [\"23652583\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Role of EB1 acetylation in vivo not fully resolved\", \"Integration with mitotic functions unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified two E3 ligases (ASB7, c-Cbl) and MT-protective stabilization controlling DDA3 abundance, establishing degradation as a key regulator of Kif2a recruitment and spindle integrity.\",\n      \"evidence\": \"Ubiquitination assays, co-IP, siRNA, epistasis rescue, immunofluorescence\",\n      \"pmids\": [\"27697924\", \"31722512\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"c-Cbl E3 activity on DDA3 inferred rather than directly assayed\", \"Cell-cycle timing of degradation not fully resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Revealed antagonistic regulators (Mdp3/MAP7D3, ANKRD53) and the Ska1 link, building a balanced network that tunes DDA3-dependent Kif2a recruitment and minus-end dynamics.\",\n      \"evidence\": \"Co-IP, MS/proteomics, siRNA epistasis, immunofluorescence, live imaging, rescue\",\n      \"pmids\": [\"27284004\", \"26820536\", \"26797278\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding interfaces not mapped for all partners\", \"Single-lab co-IP for several interactions\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Opened a metabolic axis: PSRC1 promotes macrophage cholesterol efflux and suppresses atherosclerosis via β-catenin/PPARγ/LXRα activation.\",\n      \"evidence\": \"Adenoviral overexpression in RAW264.7 and apoE−/− mice, cholesterol efflux assay, Western blot, ELISA, histology\",\n      \"pmids\": [\"29378206\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic link between MT function and lipid metabolism unestablished\", \"Overexpression-based, single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established loss-of-function PSRC1 phenotypes in cholesterol homeostasis, implicating ERα-dependent FMO3 regulation and the gut-microbiota–TMAO axis in its anti-atherosclerotic role.\",\n      \"evidence\": \"PSRC1-KO/OE macrophages and mice, reverse cholesterol transport, multi-omics, FMT, ERα inhibitor rescue\",\n      \"pmids\": [\"35690006\", \"35613310\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular target of PSRC1 in this pathway unknown\", \"Connection to the cytoskeletal function unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended the spindle function to meiosis, showing PSRC1 is required for normal oocyte spindle assembly, kinetochore–MT attachment, and euploidy.\",\n      \"evidence\": \"siRNA knockdown, mRNA overexpression, immunofluorescence, Taxol/nocodazole, Western blot in mouse oocytes\",\n      \"pmids\": [\"40810374\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether meiotic role uses the same Kif2a/EB1 machinery not tested\", \"Single study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PSRC1's microtubule-scaffolding function mechanistically connects to its metabolic and transcriptional roles, and whether a structural basis exists for its MT and partner binding, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of PSRC1 or its MT/EB1/Kif2a interfaces\", \"No unified mechanism linking spindle and cholesterol functions\", \"Human disease causation not directly demonstrated in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [2, 4, 6, 9, 10, 11]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 11, 15]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [4, 5, 13, 14]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [9, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [2, 4, 6, 10, 11]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [4, 6, 20]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [4, 8, 12, 13, 14, 15, 17]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [16, 18, 19]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 16]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"KIF2A\", \"EB1 (MAPRE1)\", \"EB3 (MAPRE3)\", \"MCAK (KIF2C)\", \"SKA1\", \"MAP7D3\", \"ANKRD53\", \"ASPP2 (TP53BP2)\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":9,"faith_total":9,"faith_pct":100.0}}