{"gene":"FKBPL","run_date":"2026-04-28T17:46:03","timeline":{"discoveries":[{"year":2005,"finding":"FKBPL (WISp39) stabilizes newly synthesized p21(WAF1/CIP1) by preventing its proteasomal degradation; FKBPL, p21, and Hsp90 form a trimeric complex in vivo, and the interaction with Hsp90 via the C-terminal TPR domain is required for p21 stabilization.","method":"Co-immunoprecipitation, point mutagenesis of TPR domain, siRNA knockdown, in vivo complex formation assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 — reciprocal Co-IP, mutagenesis of active domain, siRNA rescue, multiple orthogonal methods in single study","pmids":["15664193"],"is_preprint":false},{"year":2005,"finding":"FKBPL (WISp39) downregulation by siRNA prevents accumulation of p21 and cell cycle arrest after ionizing radiation, placing FKBPL in the p53-dependent G2/M checkpoint pathway.","method":"siRNA knockdown, clonogenic survival, cell cycle analysis after ionizing radiation","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — clean KD with defined cell cycle phenotype, replicated in multiple assays","pmids":["15664193"],"is_preprint":false},{"year":2010,"finding":"FKBPL interacts with estrogen receptor alpha (ERα) and regulates its protein levels; FKBPL overexpression increases sensitivity to antiestrogens tamoxifen and fulvestrant, while FKBPL knockdown decreases p21WAF1 levels and increases ERα phosphorylation at Ser118.","method":"Stable overexpression, siRNA knockdown, proliferation assays, western blotting for ERα phosphorylation","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2-3 — defined cellular phenotypes with mechanistic readouts but no direct binding assay shown","pmids":["20103631"],"is_preprint":false},{"year":2011,"finding":"FKBPL inhibits endothelial cell migration, tubule formation, and angiogenesis via the cell-surface receptor CD44; siRNA-mediated CD44 knockdown abrogated the antiangiogenic activity of FKBPL and its peptide AD-01.","method":"Recombinant protein assays (migration, tubule formation, aortic ring), in vivo sponge/intravital models, CD44 siRNA epistasis, xenograft tumor models","journal":"Clinical cancer research","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal in vitro and in vivo assays, CD44 epistasis confirmed in cell lines with differing CD44 status","pmids":["21364036"],"is_preprint":false},{"year":2013,"finding":"FKBPL and its peptide AD-01 bind to the CD44 receptor and inhibit tumor cell migration in a CD44-dependent manner; CD44 knockdown abrogated AD-01 binding and anti-migratory activity. Downstream of CD44, FKBPL/AD-01 inhibit Rac-1 activity, upregulate RhoA, profilin and vinculin, and induce cortical actin rearrangement.","method":"siRNA knockdown, FKBPL stable overexpression, cell migration assays, Rac-1 activity assay, immunofluorescence for actin cytoskeleton","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 — direct binding confirmed, CD44 epistasis, downstream pathway mapped with multiple readouts","pmids":["23457460"],"is_preprint":false},{"year":2013,"finding":"RBCK1 is identified as an FKBPL-interacting protein that regulates FKBPL stability via ubiquitination at the post-translational level; RBCK1, FKBPL, and ERα co-exist in Hsp90 chaperone complexes and co-associate at the pS2 promoter to regulate pS2 expression.","method":"Co-immunoprecipitation, siRNA knockdown, stable overexpression, ubiquitination assay, chromatin immunoprecipitation (ChIP)","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, ChIP, ubiquitination assay, and functional rescue provide multiple orthogonal lines of evidence","pmids":["23912458"],"is_preprint":false},{"year":2013,"finding":"FKBPL and its peptide AD-01 inhibit breast cancer stem cells (BCSCs) via a CD44-dependent mechanism, reducing mammosphere-forming efficiency and stem cell marker expression (Nanog, Oct4, Sox2), and inducing BCSC differentiation; additive inhibition was seen with the Notch inhibitor DAPT.","method":"Mammosphere assays, flow cytometry, FKBPL overexpression/knockdown, qPCR for stem cell markers, in vivo tumor initiation assay","journal":"Clinical cancer research","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal assays in vitro and in vivo, epistasis with Notch inhibitor","pmids":["23741069"],"is_preprint":false},{"year":2015,"finding":"FKBPL is essential for murine vascular development (Fkbpl knockout is embryonic lethal before E8.5); Fkbpl heterozygous mice exhibit proangiogenic phenotypes. In zebrafish, zFkbpl knockdown disrupts vasculature, rescued by hFKBPL, and this rescue is abrogated by co-knockdown of zCd44, establishing CD44 dependency in vivo.","method":"Knockout mouse generation, heterozygote vascular analysis, zebrafish morpholino knockdown, rescue with human FKBPL, aortic ring and sponge assays","journal":"Arteriosclerosis, thrombosis, and vascular biology","confidence":"High","confidence_rationale":"Tier 2 — genetic loss-of-function in two model organisms, epistasis with CD44 in vivo rescue experiment","pmids":["25767277"],"is_preprint":false},{"year":2015,"finding":"FKBPL is secreted by endothelial cells and fibroblasts; this secretion is specifically downregulated by hypoxia but not by VEGF or IL-8, suggesting hypoxia-dependent regulation of extracellular FKBPL function.","method":"ELISA of conditioned media, siRNA knockdown, hypoxia/cytokine treatment experiments","journal":"Arteriosclerosis, thrombosis, and vascular biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct secretion measurement but mechanism of hypoxia-mediated downregulation not fully resolved","pmids":["25767277"],"is_preprint":false},{"year":2015,"finding":"WISp39 (FKBPL) binds phosphorylated Coronin 1B and, via interaction with Hsp90, forms a complex with Slingshot phosphatase (SSH) to dephosphorylate and activate Cofilin; WISp39 also regulates Arp2/3 complex localization at the leading edge to control directional cell migration.","method":"Co-immunoprecipitation, siRNA knockdown, rescue by overexpression of Coronin 1B + constitutively active Cofilin, immunofluorescence for Arp2/3 localization","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, phosphorylation-specific interaction, genetic rescue with constitutively active Cofilin mutant, multiple orthogonal methods","pmids":["25800056"],"is_preprint":false},{"year":2019,"finding":"FKBPL overexpression or treatment with FKBPL-based peptides (AD-01, ALM201) inhibits cancer stem cells and breast cancer metastasis via downregulation of DLL4 and Notch4 protein and/or mRNA expression, in addition to CD44 modulation.","method":"Overexpression, peptide treatment, qRT-PCR, western blotting for DLL4/Notch4, in vivo metastasis and limiting dilution assays","journal":"BMC cancer","confidence":"Medium","confidence_rationale":"Tier 2-3 — in vitro and in vivo evidence, multiple readouts, but mechanistic link to DLL4/Notch4 established primarily by expression modulation","pmids":["30975104"],"is_preprint":false},{"year":2019,"finding":"ALM201 (FKBPL-based peptide) targets the CD44/STAT3 pathway in ovarian cancer and inhibits cancer stem cells by inducing differentiation, as well as disrupting angiogenesis in vascularized tumors.","method":"In vitro CSC assays, xenograft models, RNAseq, ELISA, western blotting","journal":"British journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple in vitro and in vivo assays, CD44/STAT3 pathway identification via RNAseq","pmids":["31772325"],"is_preprint":false},{"year":2021,"finding":"FKBPL overexpression in endothelial cells inhibits tubule formation under high glucose conditions; FKBPL knockdown reduces VE-cadherin and impairs endothelial barrier function, placing FKBPL in the regulation of endothelial integrity.","method":"FKBPL overexpression, siRNA knockdown, tubule formation assay, VE-cadherin western blotting, endothelial barrier assay","journal":"Frontiers in endocrinology","confidence":"Medium","confidence_rationale":"Tier 2-3 — clean KD/OE with defined endothelial phenotypes, single lab","pmids":["34149611"],"is_preprint":false},{"year":2024,"finding":"Cytosolic FKBPL functions as an ER-phagy regulator by acting as a scaffold connecting ER-resident CKAP4 to LC3/GABARAPs; FKBPL overexpression triggers ER fragmentation and ER-phagy, and ER-phagy-inducing conditions increase FKBPL-CKAP4 interaction followed by FKBPL oligomerization at the ER. FKBPL-CKAP4 deficiency leads to Golgi disassembly, lysosome impairment, increased ER-derived secretory vesicles, and enhanced cytosolic protein secretion via microvesicle shedding.","method":"Gain-of-function screen, Co-immunoprecipitation, overexpression/knockdown, live imaging, LC3/GABARAP interaction assays, ER fragmentation assays, secretory vesicle analysis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 — phenotype-based screen, reciprocal Co-IP, multiple orthogonal functional assays, identification of novel scaffold mechanism","pmids":["39251576"],"is_preprint":false},{"year":2026,"finding":"FKBPL knockdown in human aortic endothelial cells reduces VE-cadherin and impairs endothelial barrier; FKBPL overexpression in high-glucose conditions reduces angiogenesis by inhibiting FGF and PDGF pathways and activating proinflammatory pathways (TGF-β, leukocyte migration, IL-7 signaling), likely via CD44, upregulating miR-29b-3p and miR-302b-5p.","method":"Fkbpl transgenic mice (systemic loss), streptozotocin-induced diabetes model, siRNA knockdown, FKBPL overexpression, transcriptomic/proteomic pathway analysis, miRNA profiling","journal":"Arteriosclerosis, thrombosis, and vascular biology","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo transgenic model combined with in vitro mechanistic assays; pathway placement via multi-omic analysis","pmids":["41674464"],"is_preprint":false},{"year":2025,"finding":"AD-01 (FKBPL-based peptide) protects endothelial cells from hypoxia-induced dysfunction by stabilizing HIF-1α signaling and normalizing VE-cadherin and CD31 expression; proteomic analysis identified collagen alpha-1(XIX) and JCAD as downstream targets mediating vascular integrity effects.","method":"3D microfluidics model, siRNA knockdown, FKBPL overexpression, immunofluorescence, LC-MS/MS proteomics, hindlimb ischemia mouse model","journal":"Journal of translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 — multiple complementary methods including proteomics and in vivo model; mechanism partially elucidated","pmids":["40069829"],"is_preprint":false},{"year":2010,"finding":"FKBPL enhances androgen receptor (AR) transcriptional activity in reporter assays, suggesting a co-chaperone role for AR signaling in the testis; mutations in FKBPL are associated with azoospermia.","method":"AR reporter assay in vitro, RT-PCR/immunohistochemistry in mouse/human testis, patient mutation sequencing","journal":"Reproductive biology and endocrinology","confidence":"Medium","confidence_rationale":"Tier 3 — reporter assay establishes functional interaction, but mechanism not fully dissected; supported by clinical mutation data","pmids":["20210997"],"is_preprint":false},{"year":2000,"finding":"Repression of FKBPL (then called DIR1 in the radiation biology context) using antisense oligonucleotides increases the rate of DNA single-strand break repair and clonogenic cell survival after X-ray irradiation in radioresistant cell lines, implicating FKBPL in the DNA damage response and induced radioresistance.","method":"Antisense oligonucleotide knockdown, alkaline comet assay for SSB repair, clonogenic survival assay","journal":"International journal of radiation biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — functional knockdown with two orthogonal readouts in multiple cell lines; mechanism downstream of FKBPL not fully resolved","pmids":["10866283"],"is_preprint":false}],"current_model":"FKBPL is a multifunctional immunophilin-like scaffold protein that: (1) stabilizes p21(WAF1/CIP1) by recruiting Hsp90 into a trimeric complex to prevent proteasomal degradation and enforce the G2/M checkpoint; (2) acts extracellularly as a potent antiangiogenic factor by binding CD44 to promote cortical actin remodeling and inhibit endothelial and tumor cell migration via Rac1 suppression/RhoA upregulation; (3) functions intracellularly as an ER-phagy scaffold by connecting ER-resident CKAP4 to LC3/GABARAPs to drive ER fragmentation and autophagy, while its deficiency enhances protein secretion via microvesicle shedding; (4) co-chaperones steroid receptors (ERα, AR, GR) within Hsp90 complexes, with its stability controlled by RBCK1-mediated ubiquitination; and (5) inhibits cancer stem cell self-renewal and metastasis through downregulation of DLL4/Notch4 signaling downstream of CD44."},"narrative":{"teleology":[{"year":2000,"claim":"The earliest functional evidence established that FKBPL participates in the DNA damage response, as its repression enhanced single-strand break repair and radioresistance, raising the question of how an immunophilin-like protein interfaces with genotoxic stress pathways.","evidence":"Antisense oligonucleotide knockdown in irradiated cell lines with comet assay and clonogenic survival readouts","pmids":["10866283"],"confidence":"Medium","gaps":["Downstream mechanism linking FKBPL to SSB repair not identified","No direct target in the repair pathway established"]},{"year":2005,"claim":"The molecular mechanism was resolved: FKBPL stabilizes newly synthesized p21 by forming a trimeric complex with Hsp90 via its TPR domain, preventing proteasomal degradation of p21 and thereby enabling the G2/M checkpoint after ionizing radiation — connecting the earlier radiobiology observation to a defined chaperone-client pathway.","evidence":"Reciprocal co-immunoprecipitation, TPR domain point mutagenesis, siRNA knockdown with cell cycle analysis after irradiation","pmids":["15664193"],"confidence":"High","gaps":["Whether FKBPL stabilizes p21 independently of p53 not tested","Structural basis of trimeric complex unknown"]},{"year":2010,"claim":"FKBPL's Hsp90-dependent co-chaperone role was extended to steroid hormone receptors: it interacts with ERα to modulate antiestrogen sensitivity and enhances AR transcriptional activity, broadening its function beyond cell cycle regulation to hormone signaling.","evidence":"Stable overexpression/knockdown with western blotting for ERα and p21 in breast cancer cells; AR reporter assay in vitro with patient mutation data","pmids":["20103631","20210997"],"confidence":"Medium","gaps":["Direct FKBPL–ERα binding assay not shown","Mechanism by which FKBPL modulates ERα phosphorylation at Ser118 not resolved","AR co-chaperone mechanism inferred from reporter assay only"]},{"year":2011,"claim":"A second major axis of FKBPL function was uncovered: extracellular FKBPL acts as an antiangiogenic factor by binding CD44, with CD44 knockdown abrogating its effects on endothelial migration and tubule formation, establishing CD44 as the obligate receptor.","evidence":"Recombinant FKBPL/AD-01 peptide in migration, tubule formation, aortic ring, and in vivo sponge assays with CD44 siRNA epistasis","pmids":["21364036"],"confidence":"High","gaps":["Binding site on CD44 not mapped","How FKBPL reaches the extracellular space mechanistically was unclear at this stage"]},{"year":2013,"claim":"The downstream signaling cascade of the FKBPL–CD44 axis was delineated: FKBPL suppresses Rac1 activity, upregulates RhoA, profilin, and vinculin, and induces cortical actin rearrangement, explaining its anti-migratory effects; simultaneously, FKBPL was shown to regulate cancer stem cell self-renewal and differentiation via CD44 and in conjunction with Notch signaling.","evidence":"CD44 siRNA epistasis, Rac1 activity assays, immunofluorescence for actin cytoskeleton, mammosphere assays with Notch inhibitor DAPT epistasis, in vivo tumor initiation assays","pmids":["23457460","23741069"],"confidence":"High","gaps":["Whether Rac1 inhibition is direct or indirect not resolved","Precise molecular link between CD44 engagement and Notch pathway modulation unknown"]},{"year":2013,"claim":"FKBPL's own post-translational regulation was elucidated: RBCK1 ubiquitinates FKBPL, and the two co-exist with ERα in Hsp90 complexes and co-associate at the pS2 promoter, revealing a feedback mechanism controlling FKBPL protein levels within steroid receptor complexes.","evidence":"Reciprocal co-immunoprecipitation, ubiquitination assay, chromatin immunoprecipitation at pS2 promoter","pmids":["23912458"],"confidence":"High","gaps":["Ubiquitination site on FKBPL not mapped","Whether RBCK1-mediated degradation is the dominant turnover pathway in vivo unknown"]},{"year":2015,"claim":"Genetic loss-of-function in two organisms confirmed FKBPL as essential for vascular development: Fkbpl knockout mice die before E8.5, zebrafish knockdown disrupts vasculature in a CD44-dependent manner, and FKBPL secretion by endothelial cells is specifically downregulated by hypoxia, linking microenvironmental oxygen sensing to FKBPL bioavailability.","evidence":"Knockout mouse, zebrafish morpholino with human FKBPL rescue and CD44 co-knockdown, ELISA of conditioned media under hypoxia","pmids":["25767277"],"confidence":"High","gaps":["Mechanism of hypoxia-mediated secretion downregulation not resolved","Whether embryonic lethality is due to vascular or other defects not fully dissected"]},{"year":2015,"claim":"An intracellular cytoskeletal regulatory circuit was mapped: FKBPL binds phosphorylated Coronin 1B and, through Hsp90, assembles a complex with Slingshot phosphatase to activate Cofilin and regulate Arp2/3 localization at the leading edge, providing a mechanism for its control of directional cell migration.","evidence":"Reciprocal co-immunoprecipitation for phospho-Coronin 1B, siRNA knockdown with rescue by constitutively active Cofilin, immunofluorescence for Arp2/3","pmids":["25800056"],"confidence":"High","gaps":["Relationship between this intracellular pathway and the extracellular CD44-mediated anti-migratory function not integrated","Whether Coronin 1B-dependent mechanism operates in endothelial versus tumor cells not tested"]},{"year":2019,"claim":"The cancer stem cell mechanism was refined: FKBPL and its peptides inhibit metastasis by downregulating DLL4 and Notch4 expression downstream of CD44, and the CD44/STAT3 pathway was identified as a mediator in ovarian cancer, extending the stem cell regulatory axis beyond breast cancer.","evidence":"qRT-PCR and western blotting for DLL4/Notch4, in vivo metastasis and limiting dilution assays; RNAseq pathway analysis in ovarian cancer xenografts","pmids":["30975104","31772325"],"confidence":"Medium","gaps":["DLL4/Notch4 modulation shown at expression level only; direct signaling mechanism not established","Whether STAT3 activation is directly downstream of CD44 or involves intermediates is not resolved"]},{"year":2024,"claim":"A novel function was discovered: cytosolic FKBPL acts as an ER-phagy scaffold by connecting ER-resident CKAP4 to LC3/GABARAPs, driving ER fragmentation; its deficiency leads to Golgi disassembly, lysosome impairment, and enhanced cytosolic protein secretion via microvesicle shedding, fundamentally expanding FKBPL's role to organelle homeostasis.","evidence":"Gain-of-function screen, reciprocal co-immunoprecipitation, live imaging, LC3/GABARAP interaction assays, ER fragmentation and secretory vesicle analysis","pmids":["39251576"],"confidence":"High","gaps":["Whether ER-phagy and CD44-mediated extracellular functions are coordinated is unknown","Structural basis of FKBPL oligomerization at the ER not resolved","How FKBPL is partitioned between cytosolic ER-phagy and Hsp90 chaperone functions is unclear"]},{"year":2025,"claim":"The vascular protective function of FKBPL was extended to diabetic and ischemic contexts: FKBPL modulates endothelial barrier integrity through VE-cadherin regulation, influences FGF/PDGF and proinflammatory pathways under high glucose, and its peptide AD-01 stabilizes HIF-1α signaling during hypoxia, identifying collagen alpha-1(XIX) and JCAD as downstream mediators.","evidence":"Transgenic mouse diabetes model, siRNA/overexpression in endothelial cells, transcriptomic/proteomic pathway analysis, 3D microfluidic hypoxia model, hindlimb ischemia mouse model","pmids":["41674464","40069829","34149611"],"confidence":"Medium","gaps":["Mechanisms linking FKBPL to HIF-1α stabilization not directly established","Whether collagen alpha-1(XIX) and JCAD are direct or indirect targets unknown","Contribution of specific miRNAs (miR-29b-3p, miR-302b-5p) to FKBPL-mediated effects requires validation"]},{"year":null,"claim":"Key unresolved questions include: how FKBPL is partitioned among its diverse intracellular (ER-phagy, Hsp90 co-chaperoning) and extracellular (CD44-mediated antiangiogenic) functions; the structural basis of FKBPL interactions with Hsp90, CKAP4, and CD44; and whether its roles in ER-phagy, protein secretion, and vascular biology are mechanistically integrated.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of FKBPL in any complex","Mechanism of FKBPL secretion unresolved","Integration of ER-phagy scaffold and CD44 antiangiogenic functions not explored"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,5,9,13]},{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[0,5,16]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,4,6]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[4,9]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,9,13]},{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[3,8]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[13]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,4,6,10,11]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[13]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[7]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,5]}],"complexes":["FKBPL–Hsp90–p21 trimeric complex","RBCK1–FKBPL–ERα–Hsp90 complex","FKBPL–Coronin 1B–Hsp90–SSH complex"],"partners":["HSP90AA1","CDKN1A","CD44","RBCK1","CKAP4","CORO1B","ESR1","AR"],"other_free_text":[]},"mechanistic_narrative":"FKBPL is a multifunctional immunophilin-like scaffold protein that operates at the intersection of protein quality control, cell cycle regulation, angiogenesis, and selective autophagy. Intracellularly, FKBPL recruits Hsp90 via its C-terminal TPR domain to form a trimeric complex with p21(WAF1/CIP1), stabilizing newly synthesized p21 against proteasomal degradation and thereby enforcing the p53-dependent G2/M checkpoint after DNA damage [PMID:15664193]; it also scaffolds Hsp90-dependent complexes containing steroid receptors (ERα, AR) and the E3 ligase RBCK1, which ubiquitinates FKBPL to regulate its own stability [PMID:23912458, PMID:20103631, PMID:20210997]. Extracellularly, FKBPL functions as an antiangiogenic factor by binding the CD44 receptor to suppress Rac1, activate RhoA, and induce cortical actin remodeling, thereby inhibiting endothelial and tumor cell migration, tubule formation, and cancer stem cell self-renewal through downstream modulation of DLL4/Notch4 signaling [PMID:21364036, PMID:23457460, PMID:23741069, PMID:25767277]. FKBPL additionally serves as an ER-phagy scaffold that bridges ER-resident CKAP4 to LC3/GABARAPs to drive ER fragmentation and autophagy, with its deficiency leading to enhanced protein secretion via microvesicle shedding [PMID:39251576]."},"prefetch_data":{"uniprot":{"accession":"Q9UIM3","full_name":"FK506-binding protein-like","aliases":["WAF-1/CIP1 stabilizing protein 39","WISp39"],"length_aa":349,"mass_kda":38.2,"function":"May be involved in response to X-ray. Regulates p21 protein stability by binding to Hsp90 and p21","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9UIM3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FKBPL","classification":"Not Classified","n_dependent_lines":57,"n_total_lines":1208,"dependency_fraction":0.04718543046357616},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FKBPL","total_profiled":1310},"omim":[{"mim_id":"617076","title":"FK506-BINDING PROTEIN-LIKE; FKBPL","url":"https://www.omim.org/entry/617076"},{"mim_id":"610924","title":"RANBP-TYPE AND C3HC4-TYPE ZINC FINGER-CONTAINING 1; RBCK1","url":"https://www.omim.org/entry/610924"},{"mim_id":"138040","title":"NUCLEAR RECEPTOR SUBFAMILY 3, GROUP C, MEMBER 1; NR3C1","url":"https://www.omim.org/entry/138040"},{"mim_id":"116899","title":"CYCLIN-DEPENDENT KINASE INHIBITOR 1A; CDKN1A","url":"https://www.omim.org/entry/116899"},{"mim_id":"107269","title":"CD44 ANTIGEN; CD44","url":"https://www.omim.org/entry/107269"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Mitotic spindle","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FKBPL"},"hgnc":{"alias_symbol":["DIR1","NG7","WISp39"],"prev_symbol":[]},"alphafold":{"accession":"Q9UIM3","domains":[{"cath_id":"3.10.50.40","chopping":"93-196","consensus_level":"high","plddt":87.7718,"start":93,"end":196},{"cath_id":"1.20.58","chopping":"198-265","consensus_level":"medium","plddt":92.7709,"start":198,"end":265},{"cath_id":"1.25.40.10","chopping":"278-349","consensus_level":"medium","plddt":95.6949,"start":278,"end":349}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UIM3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UIM3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UIM3-F1-predicted_aligned_error_v6.png","plddt_mean":77.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FKBPL","jax_strain_url":"https://www.jax.org/strain/search?query=FKBPL"},"sequence":{"accession":"Q9UIM3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UIM3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UIM3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UIM3"}},"corpus_meta":[{"pmid":"23602565","id":"PMC_23602565","title":"A feedback regulatory loop between G3P and lipid transfer proteins DIR1 and AZI1 mediates azelaic-acid-induced systemic immunity.","date":"2013","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/23602565","citation_count":148,"is_preprint":false},{"pmid":"15664193","id":"PMC_15664193","title":"Regulation of p21(WAF1/CIP1) stability by WISp39, a Hsp90 binding TPR protein.","date":"2005","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/15664193","citation_count":113,"is_preprint":false},{"pmid":"22694956","id":"PMC_22694956","title":"Genome-wide association study of age-related macular degeneration identifies associated variants in the TNXB-FKBPL-NOTCH4 region of chromosome 6p21.3.","date":"2012","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22694956","citation_count":81,"is_preprint":false},{"pmid":"23847635","id":"PMC_23847635","title":"Long distance movement of DIR1 and investigation of the role of DIR1-like during systemic acquired resistance in Arabidopsis.","date":"2013","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/23847635","citation_count":80,"is_preprint":false},{"pmid":"18552128","id":"PMC_18552128","title":"The structure of \"defective in induced resistance\" protein of Arabidopsis thaliana, DIR1, reveals a new type of lipid transfer protein.","date":"2008","source":"Protein science : a publication of the Protein Society","url":"https://pubmed.ncbi.nlm.nih.gov/18552128","citation_count":69,"is_preprint":false},{"pmid":"29896854","id":"PMC_29896854","title":"Low-pH production of d-lactic acid using newly isolated acid tolerant yeast Pichia kudriavzevii NG7.","date":"2018","source":"Biotechnology and bioengineering","url":"https://pubmed.ncbi.nlm.nih.gov/29896854","citation_count":58,"is_preprint":false},{"pmid":"23741069","id":"PMC_23741069","title":"Targeting treatment-resistant breast cancer stem cells with FKBPL and its peptide derivative, AD-01, via the CD44 pathway.","date":"2013","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/23741069","citation_count":57,"is_preprint":false},{"pmid":"30975104","id":"PMC_30975104","title":"FKBPL and its peptide derivatives inhibit endocrine therapy resistant cancer stem cells and breast cancer metastasis by downregulating DLL4 and Notch4.","date":"2019","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/30975104","citation_count":50,"is_preprint":false},{"pmid":"26419658","id":"PMC_26419658","title":"RALA-mediated delivery of FKBPL nucleic acid therapeutics.","date":"2015","source":"Nanomedicine (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/26419658","citation_count":49,"is_preprint":false},{"pmid":"21364036","id":"PMC_21364036","title":"FKBPL and peptide derivatives: novel biological agents that inhibit angiogenesis by a CD44-dependent mechanism.","date":"2011","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/21364036","citation_count":48,"is_preprint":false},{"pmid":"31772325","id":"PMC_31772325","title":"FKBPL-based peptide, ALM201, targets angiogenesis and cancer stem cells in ovarian cancer.","date":"2019","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/31772325","citation_count":44,"is_preprint":false},{"pmid":"21896186","id":"PMC_21896186","title":"Localization of DIR1 at the tissue, cellular and subcellular levels during Systemic Acquired Resistance in Arabidopsis using DIR1:GUS and DIR1:EGFP reporters.","date":"2011","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/21896186","citation_count":38,"is_preprint":false},{"pmid":"20103631","id":"PMC_20103631","title":"FKBPL regulates estrogen receptor signaling and determines response to endocrine therapy.","date":"2010","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/20103631","citation_count":37,"is_preprint":false},{"pmid":"32617576","id":"PMC_32617576","title":"Role of A Novel Angiogenesis FKBPL-CD44 Pathway in Preeclampsia Risk Stratification and Mesenchymal Stem Cell Treatment.","date":"2021","source":"The Journal of clinical endocrinology and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/32617576","citation_count":36,"is_preprint":false},{"pmid":"34149611","id":"PMC_34149611","title":"FKBPL and SIRT-1 Are Downregulated by Diabetes in Pregnancy Impacting on Angiogenesis and Endothelial Function.","date":"2021","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/34149611","citation_count":35,"is_preprint":false},{"pmid":"36652019","id":"PMC_36652019","title":"A placenta-on-a-chip model to determine the regulation of FKBPL and galectin-3 in preeclampsia.","date":"2023","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/36652019","citation_count":35,"is_preprint":false},{"pmid":"25767277","id":"PMC_25767277","title":"FKBPL is a critical antiangiogenic regulator of developmental and pathological angiogenesis.","date":"2015","source":"Arteriosclerosis, thrombosis, and vascular biology","url":"https://pubmed.ncbi.nlm.nih.gov/25767277","citation_count":34,"is_preprint":false},{"pmid":"23457460","id":"PMC_23457460","title":"The anti-migratory effects of FKBPL and its peptide derivative, AD-01: regulation of CD44 and the cytoskeletal pathway.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23457460","citation_count":34,"is_preprint":false},{"pmid":"23912458","id":"PMC_23912458","title":"Identification of RBCK1 as a novel regulator of FKBPL: implications for tumor growth and response to tamoxifen.","date":"2013","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/23912458","citation_count":33,"is_preprint":false},{"pmid":"21428958","id":"PMC_21428958","title":"The emerging role of FK506-binding proteins as cancer biomarkers: a focus on FKBPL.","date":"2011","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/21428958","citation_count":29,"is_preprint":false},{"pmid":"10866283","id":"PMC_10866283","title":"Increased repair and cell survival in cells treated with DIR1 antisense oligonucleotides: implications for induced radioresistance.","date":"2000","source":"International journal of radiation biology","url":"https://pubmed.ncbi.nlm.nih.gov/10866283","citation_count":29,"is_preprint":false},{"pmid":"20210997","id":"PMC_20210997","title":"Alterations in the steroid hormone receptor co-chaperone FKBPL are associated with male infertility: a case-control study.","date":"2010","source":"Reproductive biology and endocrinology : RB&E","url":"https://pubmed.ncbi.nlm.nih.gov/20210997","citation_count":26,"is_preprint":false},{"pmid":"22265918","id":"PMC_22265918","title":"The therapeutic and diagnostic potential of FKBPL; a novel anticancer protein.","date":"2012","source":"Drug discovery today","url":"https://pubmed.ncbi.nlm.nih.gov/22265918","citation_count":25,"is_preprint":false},{"pmid":"33303872","id":"PMC_33303872","title":"FKBPL is associated with metabolic parameters and is a novel determinant of cardiovascular disease.","date":"2020","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33303872","citation_count":25,"is_preprint":false},{"pmid":"27200039","id":"PMC_27200039","title":"Orthology Analysis and In Vivo Complementation Studies to Elucidate the Role of DIR1 during Systemic Acquired Resistance in Arabidopsis thaliana and Cucumis sativus.","date":"2016","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/27200039","citation_count":17,"is_preprint":false},{"pmid":"18790546","id":"PMC_18790546","title":"Phloem sap of tomato plants contains a DIR1 putative ortholog.","date":"2008","source":"Journal of plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/18790546","citation_count":15,"is_preprint":false},{"pmid":"38261810","id":"PMC_38261810","title":"The ERF transcription factor LTF1 activates DIR1 to control stereoselective synthesis of antiviral lignans and stress defense in Isatis indigotica roots.","date":"2023","source":"Acta pharmaceutica Sinica. B","url":"https://pubmed.ncbi.nlm.nih.gov/38261810","citation_count":13,"is_preprint":false},{"pmid":"37375593","id":"PMC_37375593","title":"Vitamins C and D Exhibit Similar Antidepressant Effects to Escitalopram Mediated by NOx and FKBPL in a Stress-Induced Mice Model.","date":"2023","source":"Nutrients","url":"https://pubmed.ncbi.nlm.nih.gov/37375593","citation_count":11,"is_preprint":false},{"pmid":"25800056","id":"PMC_25800056","title":"WISp39 binds phosphorylated Coronin 1B to regulate Arp2/3 localization and Cofilin-dependent motility.","date":"2015","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25800056","citation_count":10,"is_preprint":false},{"pmid":"36830764","id":"PMC_36830764","title":"FK506-Binding Protein like (FKBPL) Has an Important Role in Heart Failure with Preserved Ejection Fraction Pathogenesis with Potential Diagnostic Utility.","date":"2023","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/36830764","citation_count":8,"is_preprint":false},{"pmid":"39251576","id":"PMC_39251576","title":"Cytosolic FKBPL and ER-resident CKAP4 co-regulates ER-phagy and protein secretion.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39251576","citation_count":8,"is_preprint":false},{"pmid":"16820699","id":"PMC_16820699","title":"Crystallization of DIR1, a LTP2-like resistance signalling protein from Arabidopsis thaliana.","date":"2006","source":"Acta crystallographica. Section F, Structural biology and crystallization communications","url":"https://pubmed.ncbi.nlm.nih.gov/16820699","citation_count":8,"is_preprint":false},{"pmid":"17708793","id":"PMC_17708793","title":"[Effect of WISp39 on proliferation, cell cycle and apoptosis of U937 cells].","date":"2007","source":"Zhongguo shi yan xue ye xue za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/17708793","citation_count":7,"is_preprint":false},{"pmid":"40069829","id":"PMC_40069829","title":"The FKBPL-based therapeutic peptide, AD-01, protects the endothelium from hypoxia-induced damage by stabilising hypoxia inducible factor-α and inflammation.","date":"2025","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40069829","citation_count":6,"is_preprint":false},{"pmid":"34977152","id":"PMC_34977152","title":"Identification of DIR1-Dependant Cellular Responses in Guard Cell Systemic Acquired Resistance.","date":"2021","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/34977152","citation_count":6,"is_preprint":false},{"pmid":"15846062","id":"PMC_15846062","title":"A novel WISp39 protein links Hsp90 and p21 stability to the G2/M checkpoint.","date":"2005","source":"Cancer biology & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/15846062","citation_count":5,"is_preprint":false},{"pmid":"36295491","id":"PMC_36295491","title":"Loss of Expression of Antiangiogenic Protein FKBPL in Endometrioid Endometrial Carcinoma: Implications for Clinical Practice.","date":"2022","source":"Medicina (Kaunas, Lithuania)","url":"https://pubmed.ncbi.nlm.nih.gov/36295491","citation_count":4,"is_preprint":false},{"pmid":"34212559","id":"PMC_34212559","title":"A novel mutation in FK506 binding protein-like (FKBPL) causes male infertility.","date":"2021","source":"Croatian medical journal","url":"https://pubmed.ncbi.nlm.nih.gov/34212559","citation_count":3,"is_preprint":false},{"pmid":"38164287","id":"PMC_38164287","title":"Expression and role of FKBPL in lung adenocarcinoma.","date":"2024","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/38164287","citation_count":2,"is_preprint":false},{"pmid":"37337412","id":"PMC_37337412","title":"Permeabilized whole cells containing co-expressed cyclomaltodextrinase and maltooligosyltrehalose synthase facilitate the synthesis of nonreducing maltoheptaose (N-G7) from β-cyclodextrin.","date":"2023","source":"Journal of the science of food and agriculture","url":"https://pubmed.ncbi.nlm.nih.gov/37337412","citation_count":0,"is_preprint":false},{"pmid":"41674464","id":"PMC_41674464","title":"Systemic Loss of FKBPL Uncovers Diabetes-Dependent Pathways of Myocardial and Vascular Injury.","date":"2026","source":"Arteriosclerosis, thrombosis, and vascular biology","url":"https://pubmed.ncbi.nlm.nih.gov/41674464","citation_count":0,"is_preprint":false},{"pmid":"29681918","id":"PMC_29681918","title":"Corrigendum: Orthology Analysis and In Vivo Complementation Studies to Elucidate the Role of DIR1 during Systemic Acquired Resistance in Arabidopsis thaliana and Cucumis sativus.","date":"2018","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/29681918","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.05.23.595641","title":"Characterization of immunity-inducing rhizobacteria highlights diversity in plant-microbe interactions","date":"2024-05-27","source":"bioRxiv","url":"https://doi.org/10.1101/2024.05.23.595641","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":23604,"output_tokens":4443,"usd":0.068728},"stage2":{"model":"claude-opus-4-6","input_tokens":7932,"output_tokens":3707,"usd":0.198502},"total_usd":0.26723,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"FKBPL (WISp39) stabilizes newly synthesized p21(WAF1/CIP1) by preventing its proteasomal degradation; FKBPL, p21, and Hsp90 form a trimeric complex in vivo, and the interaction with Hsp90 via the C-terminal TPR domain is required for p21 stabilization.\",\n      \"method\": \"Co-immunoprecipitation, point mutagenesis of TPR domain, siRNA knockdown, in vivo complex formation assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — reciprocal Co-IP, mutagenesis of active domain, siRNA rescue, multiple orthogonal methods in single study\",\n      \"pmids\": [\"15664193\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"FKBPL (WISp39) downregulation by siRNA prevents accumulation of p21 and cell cycle arrest after ionizing radiation, placing FKBPL in the p53-dependent G2/M checkpoint pathway.\",\n      \"method\": \"siRNA knockdown, clonogenic survival, cell cycle analysis after ionizing radiation\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KD with defined cell cycle phenotype, replicated in multiple assays\",\n      \"pmids\": [\"15664193\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"FKBPL interacts with estrogen receptor alpha (ERα) and regulates its protein levels; FKBPL overexpression increases sensitivity to antiestrogens tamoxifen and fulvestrant, while FKBPL knockdown decreases p21WAF1 levels and increases ERα phosphorylation at Ser118.\",\n      \"method\": \"Stable overexpression, siRNA knockdown, proliferation assays, western blotting for ERα phosphorylation\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — defined cellular phenotypes with mechanistic readouts but no direct binding assay shown\",\n      \"pmids\": [\"20103631\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"FKBPL inhibits endothelial cell migration, tubule formation, and angiogenesis via the cell-surface receptor CD44; siRNA-mediated CD44 knockdown abrogated the antiangiogenic activity of FKBPL and its peptide AD-01.\",\n      \"method\": \"Recombinant protein assays (migration, tubule formation, aortic ring), in vivo sponge/intravital models, CD44 siRNA epistasis, xenograft tumor models\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal in vitro and in vivo assays, CD44 epistasis confirmed in cell lines with differing CD44 status\",\n      \"pmids\": [\"21364036\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"FKBPL and its peptide AD-01 bind to the CD44 receptor and inhibit tumor cell migration in a CD44-dependent manner; CD44 knockdown abrogated AD-01 binding and anti-migratory activity. Downstream of CD44, FKBPL/AD-01 inhibit Rac-1 activity, upregulate RhoA, profilin and vinculin, and induce cortical actin rearrangement.\",\n      \"method\": \"siRNA knockdown, FKBPL stable overexpression, cell migration assays, Rac-1 activity assay, immunofluorescence for actin cytoskeleton\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct binding confirmed, CD44 epistasis, downstream pathway mapped with multiple readouts\",\n      \"pmids\": [\"23457460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"RBCK1 is identified as an FKBPL-interacting protein that regulates FKBPL stability via ubiquitination at the post-translational level; RBCK1, FKBPL, and ERα co-exist in Hsp90 chaperone complexes and co-associate at the pS2 promoter to regulate pS2 expression.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, stable overexpression, ubiquitination assay, chromatin immunoprecipitation (ChIP)\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, ChIP, ubiquitination assay, and functional rescue provide multiple orthogonal lines of evidence\",\n      \"pmids\": [\"23912458\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"FKBPL and its peptide AD-01 inhibit breast cancer stem cells (BCSCs) via a CD44-dependent mechanism, reducing mammosphere-forming efficiency and stem cell marker expression (Nanog, Oct4, Sox2), and inducing BCSC differentiation; additive inhibition was seen with the Notch inhibitor DAPT.\",\n      \"method\": \"Mammosphere assays, flow cytometry, FKBPL overexpression/knockdown, qPCR for stem cell markers, in vivo tumor initiation assay\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal assays in vitro and in vivo, epistasis with Notch inhibitor\",\n      \"pmids\": [\"23741069\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"FKBPL is essential for murine vascular development (Fkbpl knockout is embryonic lethal before E8.5); Fkbpl heterozygous mice exhibit proangiogenic phenotypes. In zebrafish, zFkbpl knockdown disrupts vasculature, rescued by hFKBPL, and this rescue is abrogated by co-knockdown of zCd44, establishing CD44 dependency in vivo.\",\n      \"method\": \"Knockout mouse generation, heterozygote vascular analysis, zebrafish morpholino knockdown, rescue with human FKBPL, aortic ring and sponge assays\",\n      \"journal\": \"Arteriosclerosis, thrombosis, and vascular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic loss-of-function in two model organisms, epistasis with CD44 in vivo rescue experiment\",\n      \"pmids\": [\"25767277\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"FKBPL is secreted by endothelial cells and fibroblasts; this secretion is specifically downregulated by hypoxia but not by VEGF or IL-8, suggesting hypoxia-dependent regulation of extracellular FKBPL function.\",\n      \"method\": \"ELISA of conditioned media, siRNA knockdown, hypoxia/cytokine treatment experiments\",\n      \"journal\": \"Arteriosclerosis, thrombosis, and vascular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct secretion measurement but mechanism of hypoxia-mediated downregulation not fully resolved\",\n      \"pmids\": [\"25767277\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"WISp39 (FKBPL) binds phosphorylated Coronin 1B and, via interaction with Hsp90, forms a complex with Slingshot phosphatase (SSH) to dephosphorylate and activate Cofilin; WISp39 also regulates Arp2/3 complex localization at the leading edge to control directional cell migration.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, rescue by overexpression of Coronin 1B + constitutively active Cofilin, immunofluorescence for Arp2/3 localization\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, phosphorylation-specific interaction, genetic rescue with constitutively active Cofilin mutant, multiple orthogonal methods\",\n      \"pmids\": [\"25800056\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FKBPL overexpression or treatment with FKBPL-based peptides (AD-01, ALM201) inhibits cancer stem cells and breast cancer metastasis via downregulation of DLL4 and Notch4 protein and/or mRNA expression, in addition to CD44 modulation.\",\n      \"method\": \"Overexpression, peptide treatment, qRT-PCR, western blotting for DLL4/Notch4, in vivo metastasis and limiting dilution assays\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — in vitro and in vivo evidence, multiple readouts, but mechanistic link to DLL4/Notch4 established primarily by expression modulation\",\n      \"pmids\": [\"30975104\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ALM201 (FKBPL-based peptide) targets the CD44/STAT3 pathway in ovarian cancer and inhibits cancer stem cells by inducing differentiation, as well as disrupting angiogenesis in vascularized tumors.\",\n      \"method\": \"In vitro CSC assays, xenograft models, RNAseq, ELISA, western blotting\",\n      \"journal\": \"British journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple in vitro and in vivo assays, CD44/STAT3 pathway identification via RNAseq\",\n      \"pmids\": [\"31772325\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"FKBPL overexpression in endothelial cells inhibits tubule formation under high glucose conditions; FKBPL knockdown reduces VE-cadherin and impairs endothelial barrier function, placing FKBPL in the regulation of endothelial integrity.\",\n      \"method\": \"FKBPL overexpression, siRNA knockdown, tubule formation assay, VE-cadherin western blotting, endothelial barrier assay\",\n      \"journal\": \"Frontiers in endocrinology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — clean KD/OE with defined endothelial phenotypes, single lab\",\n      \"pmids\": [\"34149611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cytosolic FKBPL functions as an ER-phagy regulator by acting as a scaffold connecting ER-resident CKAP4 to LC3/GABARAPs; FKBPL overexpression triggers ER fragmentation and ER-phagy, and ER-phagy-inducing conditions increase FKBPL-CKAP4 interaction followed by FKBPL oligomerization at the ER. FKBPL-CKAP4 deficiency leads to Golgi disassembly, lysosome impairment, increased ER-derived secretory vesicles, and enhanced cytosolic protein secretion via microvesicle shedding.\",\n      \"method\": \"Gain-of-function screen, Co-immunoprecipitation, overexpression/knockdown, live imaging, LC3/GABARAP interaction assays, ER fragmentation assays, secretory vesicle analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — phenotype-based screen, reciprocal Co-IP, multiple orthogonal functional assays, identification of novel scaffold mechanism\",\n      \"pmids\": [\"39251576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"FKBPL knockdown in human aortic endothelial cells reduces VE-cadherin and impairs endothelial barrier; FKBPL overexpression in high-glucose conditions reduces angiogenesis by inhibiting FGF and PDGF pathways and activating proinflammatory pathways (TGF-β, leukocyte migration, IL-7 signaling), likely via CD44, upregulating miR-29b-3p and miR-302b-5p.\",\n      \"method\": \"Fkbpl transgenic mice (systemic loss), streptozotocin-induced diabetes model, siRNA knockdown, FKBPL overexpression, transcriptomic/proteomic pathway analysis, miRNA profiling\",\n      \"journal\": \"Arteriosclerosis, thrombosis, and vascular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo transgenic model combined with in vitro mechanistic assays; pathway placement via multi-omic analysis\",\n      \"pmids\": [\"41674464\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"AD-01 (FKBPL-based peptide) protects endothelial cells from hypoxia-induced dysfunction by stabilizing HIF-1α signaling and normalizing VE-cadherin and CD31 expression; proteomic analysis identified collagen alpha-1(XIX) and JCAD as downstream targets mediating vascular integrity effects.\",\n      \"method\": \"3D microfluidics model, siRNA knockdown, FKBPL overexpression, immunofluorescence, LC-MS/MS proteomics, hindlimb ischemia mouse model\",\n      \"journal\": \"Journal of translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple complementary methods including proteomics and in vivo model; mechanism partially elucidated\",\n      \"pmids\": [\"40069829\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"FKBPL enhances androgen receptor (AR) transcriptional activity in reporter assays, suggesting a co-chaperone role for AR signaling in the testis; mutations in FKBPL are associated with azoospermia.\",\n      \"method\": \"AR reporter assay in vitro, RT-PCR/immunohistochemistry in mouse/human testis, patient mutation sequencing\",\n      \"journal\": \"Reproductive biology and endocrinology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — reporter assay establishes functional interaction, but mechanism not fully dissected; supported by clinical mutation data\",\n      \"pmids\": [\"20210997\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Repression of FKBPL (then called DIR1 in the radiation biology context) using antisense oligonucleotides increases the rate of DNA single-strand break repair and clonogenic cell survival after X-ray irradiation in radioresistant cell lines, implicating FKBPL in the DNA damage response and induced radioresistance.\",\n      \"method\": \"Antisense oligonucleotide knockdown, alkaline comet assay for SSB repair, clonogenic survival assay\",\n      \"journal\": \"International journal of radiation biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — functional knockdown with two orthogonal readouts in multiple cell lines; mechanism downstream of FKBPL not fully resolved\",\n      \"pmids\": [\"10866283\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FKBPL is a multifunctional immunophilin-like scaffold protein that: (1) stabilizes p21(WAF1/CIP1) by recruiting Hsp90 into a trimeric complex to prevent proteasomal degradation and enforce the G2/M checkpoint; (2) acts extracellularly as a potent antiangiogenic factor by binding CD44 to promote cortical actin remodeling and inhibit endothelial and tumor cell migration via Rac1 suppression/RhoA upregulation; (3) functions intracellularly as an ER-phagy scaffold by connecting ER-resident CKAP4 to LC3/GABARAPs to drive ER fragmentation and autophagy, while its deficiency enhances protein secretion via microvesicle shedding; (4) co-chaperones steroid receptors (ERα, AR, GR) within Hsp90 complexes, with its stability controlled by RBCK1-mediated ubiquitination; and (5) inhibits cancer stem cell self-renewal and metastasis through downregulation of DLL4/Notch4 signaling downstream of CD44.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"FKBPL is a multifunctional immunophilin-like scaffold protein that operates at the intersection of protein quality control, cell cycle regulation, angiogenesis, and selective autophagy. Intracellularly, FKBPL recruits Hsp90 via its C-terminal TPR domain to form a trimeric complex with p21(WAF1/CIP1), stabilizing newly synthesized p21 against proteasomal degradation and thereby enforcing the p53-dependent G2/M checkpoint after DNA damage [PMID:15664193]; it also scaffolds Hsp90-dependent complexes containing steroid receptors (ERα, AR) and the E3 ligase RBCK1, which ubiquitinates FKBPL to regulate its own stability [PMID:23912458, PMID:20103631, PMID:20210997]. Extracellularly, FKBPL functions as an antiangiogenic factor by binding the CD44 receptor to suppress Rac1, activate RhoA, and induce cortical actin remodeling, thereby inhibiting endothelial and tumor cell migration, tubule formation, and cancer stem cell self-renewal through downstream modulation of DLL4/Notch4 signaling [PMID:21364036, PMID:23457460, PMID:23741069, PMID:25767277]. FKBPL additionally serves as an ER-phagy scaffold that bridges ER-resident CKAP4 to LC3/GABARAPs to drive ER fragmentation and autophagy, with its deficiency leading to enhanced protein secretion via microvesicle shedding [PMID:39251576].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"The earliest functional evidence established that FKBPL participates in the DNA damage response, as its repression enhanced single-strand break repair and radioresistance, raising the question of how an immunophilin-like protein interfaces with genotoxic stress pathways.\",\n      \"evidence\": \"Antisense oligonucleotide knockdown in irradiated cell lines with comet assay and clonogenic survival readouts\",\n      \"pmids\": [\"10866283\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream mechanism linking FKBPL to SSB repair not identified\", \"No direct target in the repair pathway established\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"The molecular mechanism was resolved: FKBPL stabilizes newly synthesized p21 by forming a trimeric complex with Hsp90 via its TPR domain, preventing proteasomal degradation of p21 and thereby enabling the G2/M checkpoint after ionizing radiation — connecting the earlier radiobiology observation to a defined chaperone-client pathway.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, TPR domain point mutagenesis, siRNA knockdown with cell cycle analysis after irradiation\",\n      \"pmids\": [\"15664193\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether FKBPL stabilizes p21 independently of p53 not tested\", \"Structural basis of trimeric complex unknown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"FKBPL's Hsp90-dependent co-chaperone role was extended to steroid hormone receptors: it interacts with ERα to modulate antiestrogen sensitivity and enhances AR transcriptional activity, broadening its function beyond cell cycle regulation to hormone signaling.\",\n      \"evidence\": \"Stable overexpression/knockdown with western blotting for ERα and p21 in breast cancer cells; AR reporter assay in vitro with patient mutation data\",\n      \"pmids\": [\"20103631\", \"20210997\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct FKBPL–ERα binding assay not shown\", \"Mechanism by which FKBPL modulates ERα phosphorylation at Ser118 not resolved\", \"AR co-chaperone mechanism inferred from reporter assay only\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"A second major axis of FKBPL function was uncovered: extracellular FKBPL acts as an antiangiogenic factor by binding CD44, with CD44 knockdown abrogating its effects on endothelial migration and tubule formation, establishing CD44 as the obligate receptor.\",\n      \"evidence\": \"Recombinant FKBPL/AD-01 peptide in migration, tubule formation, aortic ring, and in vivo sponge assays with CD44 siRNA epistasis\",\n      \"pmids\": [\"21364036\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Binding site on CD44 not mapped\", \"How FKBPL reaches the extracellular space mechanistically was unclear at this stage\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The downstream signaling cascade of the FKBPL–CD44 axis was delineated: FKBPL suppresses Rac1 activity, upregulates RhoA, profilin, and vinculin, and induces cortical actin rearrangement, explaining its anti-migratory effects; simultaneously, FKBPL was shown to regulate cancer stem cell self-renewal and differentiation via CD44 and in conjunction with Notch signaling.\",\n      \"evidence\": \"CD44 siRNA epistasis, Rac1 activity assays, immunofluorescence for actin cytoskeleton, mammosphere assays with Notch inhibitor DAPT epistasis, in vivo tumor initiation assays\",\n      \"pmids\": [\"23457460\", \"23741069\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Rac1 inhibition is direct or indirect not resolved\", \"Precise molecular link between CD44 engagement and Notch pathway modulation unknown\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"FKBPL's own post-translational regulation was elucidated: RBCK1 ubiquitinates FKBPL, and the two co-exist with ERα in Hsp90 complexes and co-associate at the pS2 promoter, revealing a feedback mechanism controlling FKBPL protein levels within steroid receptor complexes.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, ubiquitination assay, chromatin immunoprecipitation at pS2 promoter\",\n      \"pmids\": [\"23912458\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitination site on FKBPL not mapped\", \"Whether RBCK1-mediated degradation is the dominant turnover pathway in vivo unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Genetic loss-of-function in two organisms confirmed FKBPL as essential for vascular development: Fkbpl knockout mice die before E8.5, zebrafish knockdown disrupts vasculature in a CD44-dependent manner, and FKBPL secretion by endothelial cells is specifically downregulated by hypoxia, linking microenvironmental oxygen sensing to FKBPL bioavailability.\",\n      \"evidence\": \"Knockout mouse, zebrafish morpholino with human FKBPL rescue and CD44 co-knockdown, ELISA of conditioned media under hypoxia\",\n      \"pmids\": [\"25767277\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of hypoxia-mediated secretion downregulation not resolved\", \"Whether embryonic lethality is due to vascular or other defects not fully dissected\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"An intracellular cytoskeletal regulatory circuit was mapped: FKBPL binds phosphorylated Coronin 1B and, through Hsp90, assembles a complex with Slingshot phosphatase to activate Cofilin and regulate Arp2/3 localization at the leading edge, providing a mechanism for its control of directional cell migration.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation for phospho-Coronin 1B, siRNA knockdown with rescue by constitutively active Cofilin, immunofluorescence for Arp2/3\",\n      \"pmids\": [\"25800056\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relationship between this intracellular pathway and the extracellular CD44-mediated anti-migratory function not integrated\", \"Whether Coronin 1B-dependent mechanism operates in endothelial versus tumor cells not tested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The cancer stem cell mechanism was refined: FKBPL and its peptides inhibit metastasis by downregulating DLL4 and Notch4 expression downstream of CD44, and the CD44/STAT3 pathway was identified as a mediator in ovarian cancer, extending the stem cell regulatory axis beyond breast cancer.\",\n      \"evidence\": \"qRT-PCR and western blotting for DLL4/Notch4, in vivo metastasis and limiting dilution assays; RNAseq pathway analysis in ovarian cancer xenografts\",\n      \"pmids\": [\"30975104\", \"31772325\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"DLL4/Notch4 modulation shown at expression level only; direct signaling mechanism not established\", \"Whether STAT3 activation is directly downstream of CD44 or involves intermediates is not resolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A novel function was discovered: cytosolic FKBPL acts as an ER-phagy scaffold by connecting ER-resident CKAP4 to LC3/GABARAPs, driving ER fragmentation; its deficiency leads to Golgi disassembly, lysosome impairment, and enhanced cytosolic protein secretion via microvesicle shedding, fundamentally expanding FKBPL's role to organelle homeostasis.\",\n      \"evidence\": \"Gain-of-function screen, reciprocal co-immunoprecipitation, live imaging, LC3/GABARAP interaction assays, ER fragmentation and secretory vesicle analysis\",\n      \"pmids\": [\"39251576\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ER-phagy and CD44-mediated extracellular functions are coordinated is unknown\", \"Structural basis of FKBPL oligomerization at the ER not resolved\", \"How FKBPL is partitioned between cytosolic ER-phagy and Hsp90 chaperone functions is unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The vascular protective function of FKBPL was extended to diabetic and ischemic contexts: FKBPL modulates endothelial barrier integrity through VE-cadherin regulation, influences FGF/PDGF and proinflammatory pathways under high glucose, and its peptide AD-01 stabilizes HIF-1α signaling during hypoxia, identifying collagen alpha-1(XIX) and JCAD as downstream mediators.\",\n      \"evidence\": \"Transgenic mouse diabetes model, siRNA/overexpression in endothelial cells, transcriptomic/proteomic pathway analysis, 3D microfluidic hypoxia model, hindlimb ischemia mouse model\",\n      \"pmids\": [\"41674464\", \"40069829\", \"34149611\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanisms linking FKBPL to HIF-1α stabilization not directly established\", \"Whether collagen alpha-1(XIX) and JCAD are direct or indirect targets unknown\", \"Contribution of specific miRNAs (miR-29b-3p, miR-302b-5p) to FKBPL-mediated effects requires validation\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: how FKBPL is partitioned among its diverse intracellular (ER-phagy, Hsp90 co-chaperoning) and extracellular (CD44-mediated antiangiogenic) functions; the structural basis of FKBPL interactions with Hsp90, CKAP4, and CD44; and whether its roles in ER-phagy, protein secretion, and vascular biology are mechanistically integrated.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of FKBPL in any complex\", \"Mechanism of FKBPL secretion unresolved\", \"Integration of ER-phagy scaffold and CD44 antiangiogenic functions not explored\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 5, 9, 13]},\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [0, 5, 16]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 4, 6]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [4, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 9, 13]},\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [3, 8]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 4, 6, 10, 11]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [13]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"complexes\": [\n      \"FKBPL–Hsp90–p21 trimeric complex\",\n      \"RBCK1–FKBPL–ERα–Hsp90 complex\",\n      \"FKBPL–Coronin 1B–Hsp90–SSH complex\"\n    ],\n    \"partners\": [\n      \"HSP90AA1\",\n      \"CDKN1A\",\n      \"CD44\",\n      \"RBCK1\",\n      \"CKAP4\",\n      \"CORO1B\",\n      \"ESR1\",\n      \"AR\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}