{"gene":"CRIP2","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2011,"finding":"CRIP2 acts as a transcription repressor by interacting with NF-κB/p65 to inhibit its DNA-binding ability at promoter regions of proangiogenic cytokines IL6, IL8, and VEGF, thereby suppressing tumorigenesis and angiogenesis.","method":"Microcell-mediated chromosome transfer, functional complementation, co-immunoprecipitation, chromatin immunoprecipitation, in vivo tumor suppression assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, ChIP at promoters, in vivo functional complementation, replicated in multiple cancer cell lines","pmids":["21540330"],"is_preprint":false},{"year":2018,"finding":"CRIP2 interacts with HOXA9 at glycolytic gene promoters (HK2, GLUT1, PDK1) to impede HIF-1α binding and repress glycolytic gene expression, placing CRIP2 downstream of HOXA9 in a miR-365-HOXA9-HIF-1α regulatory axis.","method":"Co-immunoprecipitation, chromatin immunoprecipitation, luciferase reporter assays, in vitro and in vivo glycolysis assays, loss/gain-of-function experiments","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, ChIP at promoters, reporter assays, in vivo validation in one lab with multiple orthogonal methods","pmids":["29662084"],"is_preprint":false},{"year":2021,"finding":"CRIP2 is a nuclear copper-binding protein that receives copper from the chaperone Atox1; copper transfer induces a conformational change in CRIP2's secondary structure, promoting its ubiquitin-mediated proteasomal degradation. CRIP2 depletion (or copper-induced CRIP2 degradation) elevates ROS and activates autophagy, establishing CRIP2 as an autophagic suppressor.","method":"APEX2-based proximity labeling combined with mass spectrometry, co-immunoprecipitation, circular dichroism/secondary structure analysis, proteasome inhibitor experiments, ROS measurement, autophagy flux assays","journal":"Angewandte Chemie (International ed. in English)","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — proximity labeling + MS for interaction, biochemical copper-transfer assay, structural change validated, functional autophagy readout, multiple orthogonal methods in single study","pmids":["34550632"],"is_preprint":false},{"year":2011,"finding":"CRIP2 is localized to the nucleus in esophageal squamous cell carcinoma cells, and its overexpression induces apoptosis via activation of caspases 3 and 9.","method":"Subcellular fractionation, Western blot for active caspases, colony formation and invasion assays with CRIP2 overexpression","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — single lab, nuclear fractionation plus functional caspase readout, but limited mechanistic depth","pmids":["22154084"],"is_preprint":false},{"year":2011,"finding":"In mouse cardiomyocytes, Crip2 colocalizes with cardiac troponin T in the thin filaments of sarcomeres, suggesting a structural/organizational role at the sarcomere.","method":"Immunofluorescence co-localization in mouse heart sections","journal":"Gene expression patterns : GEP","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single immunofluorescence co-localization observation, no functional perturbation experiment performed","pmids":["21601656"],"is_preprint":false},{"year":2014,"finding":"Zebrafish Crip2 is required in AV canal endocardial cells for atrioventricular valve development; its loss leads to upregulation of ECM genes versican a and has2 without affecting bmp4, tbx2b, or notch1b expression, placing Crip2 as a repressor of ECM gene expression in the endocardial cushion.","method":"Morpholino knockdown in zebrafish, in situ hybridization for ECM and signaling gene expression, heart-looping phenotype analysis","journal":"Molecules and cells","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean loss-of-function with defined gene expression phenotypes and epistatic dissection, single lab","pmids":["24823359"],"is_preprint":false},{"year":2025,"finding":"CRIP2 interacts with cytoskeleton proteins KRT8 and VIM in endothelial cells; its loss reduces their expression, causing hyperadhesion and impaired cytoskeleton formation. CRIP2 deficiency also disrupts the VEGFA/CDC42 signaling pathway (reducing migration) and impairs proliferation via interaction with SRF through PDE10A/cAMP and PDGF/JAK/STAT/SRF signaling.","method":"Co-immunoprecipitation in HUVECs, zebrafish crip2 loss-of-function, Western blot for KRT8/VIM/CDC42/SRF pathway components, cell adhesion/migration/proliferation assays","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP for interactions, zebrafish loss-of-function, multiple signaling readouts in single lab","pmids":["40074973"],"is_preprint":false},{"year":2026,"finding":"In zebrafish, Crip2 (with Crip3) is required for HSPC emergence from hemogenic endothelium; loss of Crip2/Crip3 causes failure to repress Notch signaling during HE-to-HSPC transition. Epistasis experiments show Crip genes operate through NF-κB to limit Notch, and pharmacological Notch inhibition rescues HSPC production in crip2/crip3 double mutants.","method":"CRISPR loss-of-function alleles in zebrafish, single-cell RNA-sequencing of endothelial cells, Notch inhibitor rescue experiments, epistasis analysis","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean genetic loss-of-function, scRNA-seq, pharmacological epistasis rescue, multiple orthogonal methods in single study","pmids":["41601327"],"is_preprint":false},{"year":2009,"finding":"In undifferentiated rat olfactory precursor cells, CRIP2 is predominantly localized to the cytoplasm (whereas CRP2 is both nuclear and cytoplasmic); upon differentiation into end cells, only CRIP2 expression is retained.","method":"Western blot and immunofluorescence with specific polyclonal antibodies in olfactory precursor cells","journal":"Biochemistry. Biokhimiia","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single localization study by immunofluorescence, no functional perturbation, no mechanistic follow-up","pmids":["19364329"],"is_preprint":false},{"year":2016,"finding":"miR-449a directly targets and suppresses CRIP2; CRIP2 overexpression in MDA-MB-231 cells reduces cell viability, migration, invasion, tumor growth, and angiogenesis, with evidence that it acts via inhibiting NF-κB/p65-mediated VEGF transcription.","method":"Luciferase reporter assay for miR-449a targeting of CRIP2 3'UTR, stable CRIP2 transfection, mouse xenograft tumor growth/angiogenesis assays","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — luciferase validation of miRNA target, in vivo xenograft, functional assays; NF-κB/VEGF mechanism inferred but not directly demonstrated by ChIP in this study","pmids":["26934316"],"is_preprint":false},{"year":2025,"finding":"CRIP2 upregulation in MDA-MB-231 TNBC cells inhibits phosphorylation of p65 (NF-κB), and overexpression of MAP2K4 downregulates CRIP2 expression while promoting malignant phenotypes that are reversed by CRIP2 re-expression, placing CRIP2 downstream of MAP2K4 in an NF-κB regulatory axis.","method":"Western blot for p-p65, CCK-8/EdU/Transwell assays, gain-of-function overexpression experiments with MAP2K4 and CRIP2","journal":"Translational breast cancer research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Western blot and functional assays only, MAP2K4-CRIP2 link based on expression changes without direct binding evidence","pmids":["41210648"],"is_preprint":false},{"year":2025,"finding":"CRIP2 knockdown significantly increases the sensitivity of LNCaP and C4-2B prostate cancer cells to the PARP inhibitor olaparib, establishing CRIP2 as a mediator of olaparib resistance.","method":"In vitro drug sensitivity assays (cell viability) following CRIP2 knockdown in prostate cancer cell lines","journal":"Translational andrology and urology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single in vitro drug sensitivity assay, no mechanistic pathway delineated","pmids":["41132344"],"is_preprint":false}],"current_model":"CRIP2 is a nuclear LIM-domain protein that functions primarily as a transcriptional repressor: it physically interacts with NF-κB/p65 to block its DNA binding at proangiogenic cytokine promoters (IL6, IL8, VEGF), and cooperates with HOXA9 at glycolytic gene promoters to exclude HIF-1α, thereby suppressing both tumor angiogenesis and glycolytic reprogramming; additionally, CRIP2 is a nuclear copper-binding protein that receives copper from Atox1, undergoes conformational change and proteasomal degradation upon copper loading, and acts as a suppressor of autophagy and ROS, while in developmental contexts it represses Notch signaling (via NF-κB) to enable hematopoietic stem cell emergence and represses ECM gene expression in cardiac endocardial cushions."},"narrative":{"mechanistic_narrative":"CRIP2 is a nuclear LIM-domain protein that functions principally as a transcriptional repressor restraining angiogenic and metabolic programs in cancer [PMID:21540330, PMID:29662084]. It physically interacts with NF-κB/p65 and blocks its DNA binding at the promoters of proangiogenic cytokines IL6, IL8, and VEGF, thereby suppressing tumorigenesis and angiogenesis [PMID:21540330]. In a parallel repressive role, CRIP2 cooperates with HOXA9 at glycolytic gene promoters (HK2, GLUT1, PDK1) to impede HIF-1α binding and dampen glycolytic gene expression, situating it within a miR-365–HOXA9–HIF-1α axis [PMID:29662084]. CRIP2 is also a nuclear copper-binding protein that receives copper from the chaperone Atox1; copper loading drives a conformational change and ubiquitin-mediated proteasomal degradation of CRIP2, and its loss elevates ROS and activates autophagy, identifying CRIP2 as an autophagy suppressor [PMID:34550632]. In developmental settings, CRIP2 represses Notch signaling through NF-κB to permit hematopoietic stem/progenitor cell emergence from hemogenic endothelium [PMID:41601327] and represses ECM gene expression (versican a, has2) during atrioventricular valve formation [PMID:24823359]. In endothelial cells it additionally interacts with cytoskeletal proteins KRT8 and VIM and supports migration and proliferation through VEGFA/CDC42 and SRF-linked signaling [PMID:40074973].","teleology":[{"year":2011,"claim":"Established CRIP2's core molecular function: how a LIM-domain protein could suppress tumors was unknown, and this work showed it acts as a transcriptional repressor of NF-κB/p65 at proangiogenic cytokine promoters.","evidence":"Microcell-mediated chromosome transfer, reciprocal Co-IP, ChIP at IL6/IL8/VEGF promoters, and in vivo tumor suppression assays in cancer cell lines","pmids":["21540330"],"confidence":"High","gaps":["Structural basis of the CRIP2–p65 interaction not defined","Whether repression generalizes beyond the named cytokine promoters not established"]},{"year":2011,"claim":"Tested where CRIP2 acts and its cellular consequence; demonstrated nuclear localization in esophageal carcinoma and that overexpression triggers caspase-3/9-dependent apoptosis.","evidence":"Subcellular fractionation and Western blot for active caspases with CRIP2 overexpression in ESCC cells","pmids":["22154084"],"confidence":"Medium","gaps":["Direct transcriptional targets driving apoptosis not identified","Link between nuclear repressor activity and caspase activation not mechanistically connected"]},{"year":2011,"claim":"Probed a non-nuclear role; in mouse cardiomyocytes Crip2 colocalizes with cardiac troponin T at sarcomeric thin filaments, hinting at a structural function distinct from transcriptional repression.","evidence":"Immunofluorescence co-localization in mouse heart sections","pmids":["21601656"],"confidence":"Low","gaps":["Co-localization only, no functional perturbation","No biochemical evidence of direct sarcomeric binding"]},{"year":2014,"claim":"Asked what CRIP2 does in cardiac development; loss-of-function in zebrafish showed it represses ECM genes (versican a, has2) in AV canal endocardium required for valve formation, without affecting bmp4/tbx2b/notch1b.","evidence":"Morpholino knockdown, in situ hybridization, and heart-looping phenotype analysis in zebrafish","pmids":["24823359"],"confidence":"Medium","gaps":["Direct binding of CRIP2 at ECM gene promoters not shown","Transcriptional partners in endocardium not identified"]},{"year":2016,"claim":"Placed CRIP2 within an upstream regulatory circuit; showed miR-449a directly suppresses CRIP2 and that restoring CRIP2 reduces breast cancer growth and angiogenesis via NF-κB/p65-mediated VEGF transcription.","evidence":"Luciferase 3'UTR reporter, stable CRIP2 transfection, and mouse xenograft growth/angiogenesis assays","pmids":["26934316"],"confidence":"Medium","gaps":["NF-κB/VEGF mechanism inferred without ChIP in this study","Other miR-449a targets contributing to phenotype not excluded"]},{"year":2018,"claim":"Extended CRIP2 repressor function to metabolism; demonstrated it cooperates with HOXA9 at glycolytic promoters to exclude HIF-1α, defining a miR-365–HOXA9–HIF-1α axis controlling glycolytic reprogramming.","evidence":"Reciprocal Co-IP, ChIP at HK2/GLUT1/PDK1 promoters, luciferase reporters, and in vivo glycolysis assays","pmids":["29662084"],"confidence":"High","gaps":["Whether CRIP2 directly contacts HIF-1α or only competes via HOXA9 not resolved","Stoichiometry of the CRIP2–HOXA9 complex unknown"]},{"year":2021,"claim":"Revealed a metal-sensing dimension; APEX2 proximity labeling and biochemistry showed CRIP2 binds copper received from Atox1, undergoes conformational change and proteasomal degradation, and acts to suppress ROS and autophagy.","evidence":"APEX2 proximity labeling with MS, Co-IP, circular dichroism, proteasome inhibition, ROS measurement, and autophagy flux assays","pmids":["34550632"],"confidence":"High","gaps":["Copper-binding residues and the responsible E3 ligase not identified","Mechanistic link between CRIP2 degradation and autophagy induction undefined"]},{"year":2025,"claim":"Characterized CRIP2 in endothelial cell biology; Co-IP and zebrafish loss-of-function tied it to cytoskeletal proteins KRT8/VIM and to VEGFA/CDC42 and SRF-linked migration and proliferation signaling.","evidence":"Co-IP in HUVECs, zebrafish crip2 loss-of-function, Western blot for pathway components, and adhesion/migration/proliferation assays","pmids":["40074973"],"confidence":"Medium","gaps":["Direct versus indirect nature of multiple signaling effects not separated","Whether cytoskeletal interactions are nuclear or cytoplasmic not resolved"]},{"year":2025,"claim":"Positioned CRIP2 downstream of MAP2K4 in breast cancer; overexpression studies showed CRIP2 inhibits p65 phosphorylation and reverses MAP2K4-driven malignant phenotypes.","evidence":"Western blot for p-p65 and CCK-8/EdU/Transwell assays with MAP2K4 and CRIP2 overexpression in TNBC cells","pmids":["41210648"],"confidence":"Low","gaps":["MAP2K4–CRIP2 link based on expression changes without direct binding evidence","Mechanism of CRIP2-mediated p65 dephosphorylation not defined"]},{"year":2025,"claim":"Implicated CRIP2 in therapy response; knockdown sensitized prostate cancer cells to the PARP inhibitor olaparib, identifying it as a mediator of drug resistance.","evidence":"In vitro cell viability drug-sensitivity assays after CRIP2 knockdown in LNCaP and C4-2B cells","pmids":["41132344"],"confidence":"Low","gaps":["No mechanistic pathway linking CRIP2 to olaparib resistance delineated","Not validated in vivo"]},{"year":2026,"claim":"Defined a developmental hematopoietic role; CRISPR loss-of-function and epistasis showed Crip2 (with Crip3) is required for HSPC emergence by repressing Notch through NF-κB, with Notch inhibition rescuing the defect.","evidence":"Zebrafish CRISPR alleles, single-cell RNA-seq of endothelial cells, and pharmacological Notch-inhibitor rescue/epistasis","pmids":["41601327"],"confidence":"High","gaps":["Direct molecular target of CRIP2 within the NF-κB–Notch axis not identified","Functional redundancy with Crip3 not fully dissected"]},{"year":null,"claim":"How CRIP2's nuclear transcriptional repressor activity, copper-sensing/degradation, and cytoplasmic cytoskeletal roles are integrated into a single regulatory logic remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of CRIP2 bound to p65 or HOXA9","E3 ligase and copper-binding residues unidentified","Whether copper-dependent degradation modulates its transcriptional repressor output untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,1,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140104","term_label":"molecular carrier activity","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1,2,3]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,7,10]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[5,7]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2]}],"complexes":[],"partners":["RELA","HOXA9","ATOX1","KRT8","VIM","SRF"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P52943","full_name":"Cysteine-rich protein 2","aliases":["Protein ESP1"],"length_aa":208,"mass_kda":22.5,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/P52943/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CRIP2","classification":"Not Classified","n_dependent_lines":7,"n_total_lines":1208,"dependency_fraction":0.005794701986754967},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CRIP2","total_profiled":1310},"omim":[{"mim_id":"601183","title":"CYSTEINE-RICH INTESTINAL PROTEIN 2; CRIP2","url":"https://www.omim.org/entry/601183"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"blood vessel","ntpm":641.8},{"tissue":"heart muscle","ntpm":1152.2}],"url":"https://www.proteinatlas.org/search/CRIP2"},"hgnc":{"alias_symbol":["CRP2","ESP1"],"prev_symbol":[]},"alphafold":{"accession":"P52943","domains":[{"cath_id":"2.10.110.10","chopping":"16-61","consensus_level":"high","plddt":87.4235,"start":16,"end":61},{"cath_id":"2.10.110.10","chopping":"137-182","consensus_level":"high","plddt":88.6326,"start":137,"end":182}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P52943","model_url":"https://alphafold.ebi.ac.uk/files/AF-P52943-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P52943-F1-predicted_aligned_error_v6.png","plddt_mean":72.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CRIP2","jax_strain_url":"https://www.jax.org/strain/search?query=CRIP2"},"sequence":{"accession":"P52943","fasta_url":"https://rest.uniprot.org/uniprotkb/P52943.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P52943/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P52943"}},"corpus_meta":[{"pmid":"29662084","id":"PMC_29662084","title":"HOXA9 inhibits HIF-1α-mediated glycolysis through interacting with CRIP2 to repress cutaneous squamous cell carcinoma development.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29662084","citation_count":119,"is_preprint":false},{"pmid":"21540330","id":"PMC_21540330","title":"Cysteine-rich intestinal protein 2 (CRIP2) acts as a repressor of NF-kappaB-mediated proangiogenic cytokine transcription to suppress tumorigenesis and angiogenesis.","date":"2011","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/21540330","citation_count":72,"is_preprint":false},{"pmid":"34550632","id":"PMC_34550632","title":"APEX2-based Proximity Labeling of Atox1 Identifies CRIP2 as a Nuclear Copper-binding Protein that Regulates Autophagy Activation.","date":"2021","source":"Angewandte Chemie (International ed. in English)","url":"https://pubmed.ncbi.nlm.nih.gov/34550632","citation_count":66,"is_preprint":false},{"pmid":"26934316","id":"PMC_26934316","title":"MiR-449a promotes breast cancer progression by targeting CRIP2.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26934316","citation_count":53,"is_preprint":false},{"pmid":"21601656","id":"PMC_21601656","title":"Expression of Crip2, a LIM-domain-only protein, in the mouse cardiovascular system under physiological and pathological conditions.","date":"2011","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/21601656","citation_count":27,"is_preprint":false},{"pmid":"22154084","id":"PMC_22154084","title":"The LIM domain protein, CRIP2, promotes apoptosis in esophageal squamous cell carcinoma.","date":"2011","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/22154084","citation_count":21,"is_preprint":false},{"pmid":"24823359","id":"PMC_24823359","title":"Zebrafish Crip2 plays a critical role in atrioventricular valve development by downregulating the expression of ECM genes in the endocardial cushion.","date":"2014","source":"Molecules and cells","url":"https://pubmed.ncbi.nlm.nih.gov/24823359","citation_count":13,"is_preprint":false},{"pmid":"40074973","id":"PMC_40074973","title":"Crip2 affects vascular development by fine-tuning endothelial cell aggregation and proliferation.","date":"2025","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/40074973","citation_count":4,"is_preprint":false},{"pmid":"41601327","id":"PMC_41601327","title":"Crip2 preserves hematopoietic stem and progenitor cell production through inhibition of Notch signals.","date":"2026","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/41601327","citation_count":1,"is_preprint":false},{"pmid":"19364329","id":"PMC_19364329","title":"Polyclonal antibodies to LIM proteins CRP2 and CRIP2 reveal their subcellular localizations in olfactory precursor cells.","date":"2009","source":"Biochemistry. Biokhimiia","url":"https://pubmed.ncbi.nlm.nih.gov/19364329","citation_count":1,"is_preprint":false},{"pmid":"41132344","id":"PMC_41132344","title":"Omics integration identified CRIP2 as a key mediator of olaparib resistance in prostate cancer.","date":"2025","source":"Translational andrology and urology","url":"https://pubmed.ncbi.nlm.nih.gov/41132344","citation_count":0,"is_preprint":false},{"pmid":"41210648","id":"PMC_41210648","title":"The impact and mechanisms of CRIP2 on the biological behavior of triple-negative breast cancer cells.","date":"2025","source":"Translational breast cancer research : a journal focusing on translational research in breast cancer","url":"https://pubmed.ncbi.nlm.nih.gov/41210648","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8130,"output_tokens":3030,"usd":0.03492,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10406,"output_tokens":3975,"usd":0.075703,"stage2_stop_reason":"end_turn"},"total_usd":0.110623,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"CRIP2 acts as a transcription repressor by interacting with NF-κB/p65 to inhibit its DNA-binding ability at promoter regions of proangiogenic cytokines IL6, IL8, and VEGF, thereby suppressing tumorigenesis and angiogenesis.\",\n      \"method\": \"Microcell-mediated chromosome transfer, functional complementation, co-immunoprecipitation, chromatin immunoprecipitation, in vivo tumor suppression assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, ChIP at promoters, in vivo functional complementation, replicated in multiple cancer cell lines\",\n      \"pmids\": [\"21540330\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CRIP2 interacts with HOXA9 at glycolytic gene promoters (HK2, GLUT1, PDK1) to impede HIF-1α binding and repress glycolytic gene expression, placing CRIP2 downstream of HOXA9 in a miR-365-HOXA9-HIF-1α regulatory axis.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation, luciferase reporter assays, in vitro and in vivo glycolysis assays, loss/gain-of-function experiments\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, ChIP at promoters, reporter assays, in vivo validation in one lab with multiple orthogonal methods\",\n      \"pmids\": [\"29662084\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CRIP2 is a nuclear copper-binding protein that receives copper from the chaperone Atox1; copper transfer induces a conformational change in CRIP2's secondary structure, promoting its ubiquitin-mediated proteasomal degradation. CRIP2 depletion (or copper-induced CRIP2 degradation) elevates ROS and activates autophagy, establishing CRIP2 as an autophagic suppressor.\",\n      \"method\": \"APEX2-based proximity labeling combined with mass spectrometry, co-immunoprecipitation, circular dichroism/secondary structure analysis, proteasome inhibitor experiments, ROS measurement, autophagy flux assays\",\n      \"journal\": \"Angewandte Chemie (International ed. in English)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — proximity labeling + MS for interaction, biochemical copper-transfer assay, structural change validated, functional autophagy readout, multiple orthogonal methods in single study\",\n      \"pmids\": [\"34550632\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"CRIP2 is localized to the nucleus in esophageal squamous cell carcinoma cells, and its overexpression induces apoptosis via activation of caspases 3 and 9.\",\n      \"method\": \"Subcellular fractionation, Western blot for active caspases, colony formation and invasion assays with CRIP2 overexpression\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — single lab, nuclear fractionation plus functional caspase readout, but limited mechanistic depth\",\n      \"pmids\": [\"22154084\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"In mouse cardiomyocytes, Crip2 colocalizes with cardiac troponin T in the thin filaments of sarcomeres, suggesting a structural/organizational role at the sarcomere.\",\n      \"method\": \"Immunofluorescence co-localization in mouse heart sections\",\n      \"journal\": \"Gene expression patterns : GEP\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single immunofluorescence co-localization observation, no functional perturbation experiment performed\",\n      \"pmids\": [\"21601656\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Zebrafish Crip2 is required in AV canal endocardial cells for atrioventricular valve development; its loss leads to upregulation of ECM genes versican a and has2 without affecting bmp4, tbx2b, or notch1b expression, placing Crip2 as a repressor of ECM gene expression in the endocardial cushion.\",\n      \"method\": \"Morpholino knockdown in zebrafish, in situ hybridization for ECM and signaling gene expression, heart-looping phenotype analysis\",\n      \"journal\": \"Molecules and cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean loss-of-function with defined gene expression phenotypes and epistatic dissection, single lab\",\n      \"pmids\": [\"24823359\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CRIP2 interacts with cytoskeleton proteins KRT8 and VIM in endothelial cells; its loss reduces their expression, causing hyperadhesion and impaired cytoskeleton formation. CRIP2 deficiency also disrupts the VEGFA/CDC42 signaling pathway (reducing migration) and impairs proliferation via interaction with SRF through PDE10A/cAMP and PDGF/JAK/STAT/SRF signaling.\",\n      \"method\": \"Co-immunoprecipitation in HUVECs, zebrafish crip2 loss-of-function, Western blot for KRT8/VIM/CDC42/SRF pathway components, cell adhesion/migration/proliferation assays\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP for interactions, zebrafish loss-of-function, multiple signaling readouts in single lab\",\n      \"pmids\": [\"40074973\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In zebrafish, Crip2 (with Crip3) is required for HSPC emergence from hemogenic endothelium; loss of Crip2/Crip3 causes failure to repress Notch signaling during HE-to-HSPC transition. Epistasis experiments show Crip genes operate through NF-κB to limit Notch, and pharmacological Notch inhibition rescues HSPC production in crip2/crip3 double mutants.\",\n      \"method\": \"CRISPR loss-of-function alleles in zebrafish, single-cell RNA-sequencing of endothelial cells, Notch inhibitor rescue experiments, epistasis analysis\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic loss-of-function, scRNA-seq, pharmacological epistasis rescue, multiple orthogonal methods in single study\",\n      \"pmids\": [\"41601327\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"In undifferentiated rat olfactory precursor cells, CRIP2 is predominantly localized to the cytoplasm (whereas CRP2 is both nuclear and cytoplasmic); upon differentiation into end cells, only CRIP2 expression is retained.\",\n      \"method\": \"Western blot and immunofluorescence with specific polyclonal antibodies in olfactory precursor cells\",\n      \"journal\": \"Biochemistry. Biokhimiia\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single localization study by immunofluorescence, no functional perturbation, no mechanistic follow-up\",\n      \"pmids\": [\"19364329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"miR-449a directly targets and suppresses CRIP2; CRIP2 overexpression in MDA-MB-231 cells reduces cell viability, migration, invasion, tumor growth, and angiogenesis, with evidence that it acts via inhibiting NF-κB/p65-mediated VEGF transcription.\",\n      \"method\": \"Luciferase reporter assay for miR-449a targeting of CRIP2 3'UTR, stable CRIP2 transfection, mouse xenograft tumor growth/angiogenesis assays\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — luciferase validation of miRNA target, in vivo xenograft, functional assays; NF-κB/VEGF mechanism inferred but not directly demonstrated by ChIP in this study\",\n      \"pmids\": [\"26934316\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CRIP2 upregulation in MDA-MB-231 TNBC cells inhibits phosphorylation of p65 (NF-κB), and overexpression of MAP2K4 downregulates CRIP2 expression while promoting malignant phenotypes that are reversed by CRIP2 re-expression, placing CRIP2 downstream of MAP2K4 in an NF-κB regulatory axis.\",\n      \"method\": \"Western blot for p-p65, CCK-8/EdU/Transwell assays, gain-of-function overexpression experiments with MAP2K4 and CRIP2\",\n      \"journal\": \"Translational breast cancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Western blot and functional assays only, MAP2K4-CRIP2 link based on expression changes without direct binding evidence\",\n      \"pmids\": [\"41210648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CRIP2 knockdown significantly increases the sensitivity of LNCaP and C4-2B prostate cancer cells to the PARP inhibitor olaparib, establishing CRIP2 as a mediator of olaparib resistance.\",\n      \"method\": \"In vitro drug sensitivity assays (cell viability) following CRIP2 knockdown in prostate cancer cell lines\",\n      \"journal\": \"Translational andrology and urology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single in vitro drug sensitivity assay, no mechanistic pathway delineated\",\n      \"pmids\": [\"41132344\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CRIP2 is a nuclear LIM-domain protein that functions primarily as a transcriptional repressor: it physically interacts with NF-κB/p65 to block its DNA binding at proangiogenic cytokine promoters (IL6, IL8, VEGF), and cooperates with HOXA9 at glycolytic gene promoters to exclude HIF-1α, thereby suppressing both tumor angiogenesis and glycolytic reprogramming; additionally, CRIP2 is a nuclear copper-binding protein that receives copper from Atox1, undergoes conformational change and proteasomal degradation upon copper loading, and acts as a suppressor of autophagy and ROS, while in developmental contexts it represses Notch signaling (via NF-κB) to enable hematopoietic stem cell emergence and represses ECM gene expression in cardiac endocardial cushions.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CRIP2 is a nuclear LIM-domain protein that functions principally as a transcriptional repressor restraining angiogenic and metabolic programs in cancer [#0, #1]. It physically interacts with NF-\\u03baB/p65 and blocks its DNA binding at the promoters of proangiogenic cytokines IL6, IL8, and VEGF, thereby suppressing tumorigenesis and angiogenesis [#0]. In a parallel repressive role, CRIP2 cooperates with HOXA9 at glycolytic gene promoters (HK2, GLUT1, PDK1) to impede HIF-1\\u03b1 binding and dampen glycolytic gene expression, situating it within a miR-365\\u2013HOXA9\\u2013HIF-1\\u03b1 axis [#1]. CRIP2 is also a nuclear copper-binding protein that receives copper from the chaperone Atox1; copper loading drives a conformational change and ubiquitin-mediated proteasomal degradation of CRIP2, and its loss elevates ROS and activates autophagy, identifying CRIP2 as an autophagy suppressor [#2]. In developmental settings, CRIP2 represses Notch signaling through NF-\\u03baB to permit hematopoietic stem/progenitor cell emergence from hemogenic endothelium [#7] and represses ECM gene expression (versican a, has2) during atrioventricular valve formation [#5]. In endothelial cells it additionally interacts with cytoskeletal proteins KRT8 and VIM and supports migration and proliferation through VEGFA/CDC42 and SRF-linked signaling [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established CRIP2's core molecular function: how a LIM-domain protein could suppress tumors was unknown, and this work showed it acts as a transcriptional repressor of NF-\\u03baB/p65 at proangiogenic cytokine promoters.\",\n      \"evidence\": \"Microcell-mediated chromosome transfer, reciprocal Co-IP, ChIP at IL6/IL8/VEGF promoters, and in vivo tumor suppression assays in cancer cell lines\",\n      \"pmids\": [\"21540330\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the CRIP2\\u2013p65 interaction not defined\", \"Whether repression generalizes beyond the named cytokine promoters not established\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Tested where CRIP2 acts and its cellular consequence; demonstrated nuclear localization in esophageal carcinoma and that overexpression triggers caspase-3/9-dependent apoptosis.\",\n      \"evidence\": \"Subcellular fractionation and Western blot for active caspases with CRIP2 overexpression in ESCC cells\",\n      \"pmids\": [\"22154084\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct transcriptional targets driving apoptosis not identified\", \"Link between nuclear repressor activity and caspase activation not mechanistically connected\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Probed a non-nuclear role; in mouse cardiomyocytes Crip2 colocalizes with cardiac troponin T at sarcomeric thin filaments, hinting at a structural function distinct from transcriptional repression.\",\n      \"evidence\": \"Immunofluorescence co-localization in mouse heart sections\",\n      \"pmids\": [\"21601656\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Co-localization only, no functional perturbation\", \"No biochemical evidence of direct sarcomeric binding\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Asked what CRIP2 does in cardiac development; loss-of-function in zebrafish showed it represses ECM genes (versican a, has2) in AV canal endocardium required for valve formation, without affecting bmp4/tbx2b/notch1b.\",\n      \"evidence\": \"Morpholino knockdown, in situ hybridization, and heart-looping phenotype analysis in zebrafish\",\n      \"pmids\": [\"24823359\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding of CRIP2 at ECM gene promoters not shown\", \"Transcriptional partners in endocardium not identified\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Placed CRIP2 within an upstream regulatory circuit; showed miR-449a directly suppresses CRIP2 and that restoring CRIP2 reduces breast cancer growth and angiogenesis via NF-\\u03baB/p65-mediated VEGF transcription.\",\n      \"evidence\": \"Luciferase 3'UTR reporter, stable CRIP2 transfection, and mouse xenograft growth/angiogenesis assays\",\n      \"pmids\": [\"26934316\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"NF-\\u03baB/VEGF mechanism inferred without ChIP in this study\", \"Other miR-449a targets contributing to phenotype not excluded\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended CRIP2 repressor function to metabolism; demonstrated it cooperates with HOXA9 at glycolytic promoters to exclude HIF-1\\u03b1, defining a miR-365\\u2013HOXA9\\u2013HIF-1\\u03b1 axis controlling glycolytic reprogramming.\",\n      \"evidence\": \"Reciprocal Co-IP, ChIP at HK2/GLUT1/PDK1 promoters, luciferase reporters, and in vivo glycolysis assays\",\n      \"pmids\": [\"29662084\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether CRIP2 directly contacts HIF-1\\u03b1 or only competes via HOXA9 not resolved\", \"Stoichiometry of the CRIP2\\u2013HOXA9 complex unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealed a metal-sensing dimension; APEX2 proximity labeling and biochemistry showed CRIP2 binds copper received from Atox1, undergoes conformational change and proteasomal degradation, and acts to suppress ROS and autophagy.\",\n      \"evidence\": \"APEX2 proximity labeling with MS, Co-IP, circular dichroism, proteasome inhibition, ROS measurement, and autophagy flux assays\",\n      \"pmids\": [\"34550632\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Copper-binding residues and the responsible E3 ligase not identified\", \"Mechanistic link between CRIP2 degradation and autophagy induction undefined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Characterized CRIP2 in endothelial cell biology; Co-IP and zebrafish loss-of-function tied it to cytoskeletal proteins KRT8/VIM and to VEGFA/CDC42 and SRF-linked migration and proliferation signaling.\",\n      \"evidence\": \"Co-IP in HUVECs, zebrafish crip2 loss-of-function, Western blot for pathway components, and adhesion/migration/proliferation assays\",\n      \"pmids\": [\"40074973\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect nature of multiple signaling effects not separated\", \"Whether cytoskeletal interactions are nuclear or cytoplasmic not resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Positioned CRIP2 downstream of MAP2K4 in breast cancer; overexpression studies showed CRIP2 inhibits p65 phosphorylation and reverses MAP2K4-driven malignant phenotypes.\",\n      \"evidence\": \"Western blot for p-p65 and CCK-8/EdU/Transwell assays with MAP2K4 and CRIP2 overexpression in TNBC cells\",\n      \"pmids\": [\"41210648\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"MAP2K4\\u2013CRIP2 link based on expression changes without direct binding evidence\", \"Mechanism of CRIP2-mediated p65 dephosphorylation not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated CRIP2 in therapy response; knockdown sensitized prostate cancer cells to the PARP inhibitor olaparib, identifying it as a mediator of drug resistance.\",\n      \"evidence\": \"In vitro cell viability drug-sensitivity assays after CRIP2 knockdown in LNCaP and C4-2B cells\",\n      \"pmids\": [\"41132344\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanistic pathway linking CRIP2 to olaparib resistance delineated\", \"Not validated in vivo\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined a developmental hematopoietic role; CRISPR loss-of-function and epistasis showed Crip2 (with Crip3) is required for HSPC emergence by repressing Notch through NF-\\u03baB, with Notch inhibition rescuing the defect.\",\n      \"evidence\": \"Zebrafish CRISPR alleles, single-cell RNA-seq of endothelial cells, and pharmacological Notch-inhibitor rescue/epistasis\",\n      \"pmids\": [\"41601327\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct molecular target of CRIP2 within the NF-\\u03baB\\u2013Notch axis not identified\", \"Functional redundancy with Crip3 not fully dissected\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CRIP2's nuclear transcriptional repressor activity, copper-sensing/degradation, and cytoplasmic cytoskeletal roles are integrated into a single regulatory logic remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of CRIP2 bound to p65 or HOXA9\", \"E3 ligase and copper-binding residues unidentified\", \"Whether copper-dependent degradation modulates its transcriptional repressor output untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 1, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140104\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 2, 3]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 7, 10]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [5, 7]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RELA\", \"HOXA9\", \"ATOX1\", \"KRT8\", \"VIM\", \"SRF\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":6,"faith_total":6,"faith_pct":100.0}}