Affinage

FDFT1

Squalene synthase · UniProt P37268

Length
417 aa
Mass
48.1 kDa
Annotated
2026-06-09
44 papers in source corpus 19 papers cited in narrative 19 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

FDFT1 (squalene synthase) is the committed enzyme of sterol biosynthesis, catalyzing condensation of two farnesyl diphosphate molecules to form squalene, and its activity functions as a metabolic rheostat that sets cellular cholesterol and bile acid pools to modulate downstream growth, survival, and stress signaling (PMID:32313017, PMID:39899681). The gene was mapped to human chromosome 8p22-p23.1 (PMID:8020937), and its enzymatic function in sterol synthesis is directly demonstrated by the finding that bi-allelic somatic silencing of FDFT1 drives clonal expansion of cholesterol-dependent keratinocytes to cause porokeratosis, lesions ameliorated by topical statin treatment (PMID:38653249). In multiple cancers FDFT1 behaves as a tumor suppressor: it restrains AKT/mTOR/HIF1α signaling and aerobic glycolysis (PMID:32313017), and in hepatocellular carcinoma its cholesterol/bile-acid output suppresses HNF4A-driven ALDOB transcription, where ALDOB binds AKT1 to block its phosphorylation (PMID:39899681). FDFT1-derived cholesterol also negatively regulates autophagy via AMPK-ULK1 (PMID:42059033), suppresses NEDD4 induction through the TNFR1/NF-κB axis (PMID:39461203), and lowers ferroptosis susceptibility (PMID:40931051). FDFT1 transcription is driven by SREBP2 (PMID:39707501) and additional inputs including NeuroD1 acting through KAT2A-mediated H3K27 acetylation (PMID:40890513), while its protein level is set post-translationally by THEM6/HSP90, which shields FDFT1 from K48-ubiquitination and ER-associated degradation (PMID:40931051). When FDFT1 is suppressed, farnesyl diphosphate flux is redirected to the non-sterol prenylation branch of the mevalonate pathway, activating Ras/Rho prenylation and promoting chemoresistance (PMID:39270927).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1994 High

    Establishing the chromosomal location of the human squalene synthase gene provided the genomic anchor for all subsequent functional and disease studies.

    Evidence FISH with a YAC clone plus somatic cell hybrid PCR mapping

    PMID:8020937

    Open questions at the time
    • Mapping alone established no enzymatic or regulatory function
    • No protein-level characterization in this study
  2. 2007 Medium

    A hypomorphic Fdft1 allele linking reduced cholesterol biosynthesis to hereditary cataract demonstrated that FDFT1 activity level is physiologically dose-sensitive in vivo.

    Evidence Genetic screening and sequencing of mutant rat alleles with functional characterization

    PMID:17460354

    Open questions at the time
    • Mechanistic link between sterol depletion and cataract not resolved
    • Findings in rat strains, not human
  3. 2020 High

    Loss- and gain-of-function studies recast FDFT1 from a housekeeping enzyme into a tumor suppressor that actively restrains oncogenic AKT/mTOR/HIF1α signaling and glycolysis.

    Evidence siRNA knockdown, overexpression, glycolysis assays and xenografts in CRC; miRNA/SREBP-2-axis rescue experiments in CRC, hepatic and ovarian models

    PMID:32313017 PMID:32827918 PMID:32877662

    Open questions at the time
    • How an ER sterol enzyme mechanistically suppresses AKT/mTOR not fully resolved at this stage
    • Relative contribution of cholesterol depletion versus FPP accumulation unclear
  4. 2024 High

    Direct small-molecule binding and transcriptional mapping defined how FDFT1 is controlled and how its loss triggers cell death, identifying the TNFR1/NF-κB/NEDD4 apoptotic axis and SREBP2 as its principal transcriptional driver.

    Evidence CETSA/SPR/docking for direct artemisitene binding plus ChIP in breast cancer; RNA-seq, inhibitor (YM-53601) and knockdown in glioblastoma stem cells

    PMID:39461203 PMID:39707501

    Open questions at the time
    • Whether NEDD4 induction depends on cholesterol depletion or direct FDFT1 enzymatic activity not separated
    • SREBP2 regulation studied in single tumor context
  5. 2024 Medium

    Identification of estrogen-GSK3β-LSD1 and microRNA inputs showed FDFT1 transcription is set by hormonal and epigenetic signals, and that its suppression reroutes substrate to non-sterol prenylation to drive chemoresistance.

    Evidence CUT&RUN, Co-IP and transcriptomics in chicken theca cells; luciferase, knockdown and pathway gene expression in bladder cancer

    PMID:39270927 PMID:39595520

    Open questions at the time
    • FPP rerouting inferred from pathway gene expression, not direct metabolite flux measurement
    • Estrogen axis characterized in avian cells only
  6. 2024 High

    Discovery that bi-allelic somatic silencing of FDFT1 causes porokeratosis provided direct in-human disease evidence that FDFT1-driven cholesterol synthesis is required for normal keratinocyte homeostasis.

    Evidence Genomic and bisulfite sequencing, IHC, keratinocyte cholesterol rescue and topical statin treatment

    PMID:38653249

    Open questions at the time
    • Mechanism connecting cholesterol dependence to clonal expansion and cell-cycle change not fully resolved
  7. 2025 High

    Mechanistic dissection in HCC and TNBC defined the downstream effector axes and the post-translational control of FDFT1 — the HNF4A/ALDOB/AKT1 axis, AMPK-ULK1 autophagy suppression, and THEM6/HSP90-mediated protection from ERAD.

    Evidence Co-IP, promoter binding, metabolite quantification and pharmacological rescue in HCC; ubiquitination assays, protein half-life and ferroptosis readouts in TNBC; autophagosome imaging and AMPK-ULK1 blotting

    PMID:39899681 PMID:40890513 PMID:40931051 PMID:42059033

    Open questions at the time
    • Whether the same axes operate outside liver and breast contexts untested
    • How cholesterol level mechanistically modulates HNF4A activity not fully defined
  8. 2025 Medium

    Pharmacological and viral studies extended FDFT1's reach to statin-induced anti-tumor responses, additional non-coding RNA regulation, and modulation of viral replication state through cholesterol.

    Evidence AOM/DSS CRC model with atorvastatin; SQS inhibitors in lung cancer; piR-39980 luciferase/knockdown in tongue cancer; METTL7A-SREBP1 Co-IP in CRC; HIV-1 Tat/KSHV expression assays

    PMID:40339976 PMID:40947702 PMID:41089479 PMID:41866501 PMID:42009961

    Open questions at the time
    • KSHV/HIV link rests on expression readouts without biochemical confirmation
    • Tissue-specificity of the many regulatory inputs not reconciled into one model

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved whether FDFT1's growth-suppressive effects derive primarily from cholesterol/bile-acid depletion, from accumulation of the farnesyl-diphosphate substrate redirected to prenylation, or from a non-catalytic scaffolding role, and how its context-dependent tumor-suppressor versus stemness-promoting functions are reconciled.
  • No structural model of FDFT1 in any signaling complex in the corpus
  • Direct flux measurements separating sterol from prenylation contributions are lacking
  • Reconciliation of opposing tumor-context roles unresolved

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 2
Localization
GO:0005783 endoplasmic reticulum 1
Pathway
R-HSA-1430728 Metabolism 3 R-HSA-162582 Signal Transduction 3 R-HSA-9612973 Autophagy 2
Partners

Evidence

Reading pass · 19 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 The FDFT1 (squalene synthase) gene was mapped to human chromosome 8p22-p23.1 using fluorescence in situ hybridization (FISH) with a YAC containing the gene, confirmed by PCR of somatic cell hybrids. FISH, somatic cell hybrid PCR mapping Genomics High 8020937
2007 The Fdft1 gene in rats harbors a hypomorphic allele (Fdft1(S)) with a missense nucleotide substitution that reduces cholesterol biosynthesis function; this allele is widely prevalent across laboratory rat strains and was identified as a determinant of hereditary cataracts in the SCR rat strain. Genetic screening, sequencing, functional characterization of mutant alleles Experimental animals Medium 17460354
2020 FDFT1 acts as a tumor suppressor in colorectal cancer by negatively regulating AKT/mTOR/HIF1α signaling; fasting upregulates FDFT1 expression and inhibits aerobic glycolysis and proliferation in CRC cells through this pathway. Loss-of-function (siRNA knockdown), overexpression, in vitro proliferation/glycolysis assays, in vivo xenograft models, pathway inhibitor experiments Nature communications High 32313017
2020 Bavachinin inhibits FDFT1 expression via the AKT/mTOR/SREBP-2 pathway in HepaRG cells; overexpression of FDFT1 abolished bavachinin-induced inhibition of cholesterol synthesis, establishing FDFT1 as a downstream effector of this pathway in cholesterol regulation. Overexpression rescue experiments, Western blot, lipid accumulation assays, pathway inhibitor analysis International immunopharmacology Medium 32827918
2020 miR-4425 directly targets FDFT1 mRNA to suppress its expression; forced FDFT1 expression negates the tumorigenic properties of miR-4425 in ovarian cancer cells, establishing FDFT1 as a functional target of miR-4425. Luciferase reporter assay, Western blot, siRNA knockdown, overexpression rescue, in vivo xenograft Archives of biochemistry and biophysics High 32877662
2024 Somatic bi-allelic genetic and/or epigenetic (promoter hypermethylation) silencing of FDFT1 causes clonal expansion of FDFT1-deficient keratinocytes, resulting in porokeratosis; FDFT1-deficient keratinocytes showed cholesterol dependence for cell growth and altered cell-cycle and epidermal development gene expression. Topical statin treatment ameliorated lesions, confirming FDFT1's role in cholesterol synthesis in skin. Genomic sequencing, bisulfite sequencing (methylation analysis), IHC for FDFT1 localization in lesions, keratinocyte culture with cholesterol rescue, RT-PCR for gene expression American journal of human genetics High 38653249
2024 Artemisitene (ATT) directly binds FDFT1 in breast cancer cells, as confirmed by CETSA, SPR, and molecular docking. Knockdown of FDFT1 induced NEDD4 expression and apoptosis via the TNFR1/NF-κB pathway; FDFT1 overexpression rescued ATT-induced apoptosis. ChIP assay showed p65 (NF-κB) regulates NEDD4 transcription downstream of FDFT1. CETSA, surface plasmon resonance (SPR), molecular docking, siRNA knockdown, overexpression rescue, ChIP assay, flow cytometry, Western blot Phytomedicine High 39461203
2024 FDFT1 is transcriptionally regulated by SREBP2 (not SREBP1) in glioblastoma stem cells; FDFT1 activates the AKT pathway to regulate tumor metabolism and maintain stemness. Knockdown of FDFT1 suppressed proliferation, migration, and enhanced temozolomide sensitivity. RNA-seq, RT-qPCR, Western blot, siRNA knockdown, FDFT1 inhibitor (YM-53601), neurosphere formation assay, CCK8, transwell/wound healing assays Stem cell research & therapy Medium 39707501
2024 microRNA-146b-5p directly targets and downregulates FDFT1 in bladder cancer; FDFT1 suppression redirects its substrate (farnesyl diphosphate) toward the non-sterol branch of the mevalonate pathway, upregulating non-sterol branch genes and reducing total cholesterol, thereby promoting cisplatin resistance via activation of Ras/Rho family protein prenylation. Functional knockdown, ectopic overexpression, bioinformatics, rescue experiments, gene expression analysis of downstream pathway The international journal of biochemistry & cell biology Medium 39270927
2025 FDFT1 knockdown in HCC decreases cholesterol and bile acid levels, increases HNF4A transcriptional activity, which promotes ALDOB transcription; ALDOB then binds AKT1 and inhibits AKT1 phosphorylation, delaying HCC progression. This HNF4A/ALDOB/AKT1 axis was established as the mechanistic pathway downstream of FDFT1. siRNA knockdown, overexpression, in vitro and in vivo experiments, ChIP/promoter binding assays, co-immunoprecipitation (ALDOB-AKT1), AKT inhibitor combination, cholesterol/bile acid quantification Advanced science High 39899681
2025 NeuroD1 binds the FDFT1 promoter and activates FDFT1 transcription; this is mediated through KAT2A-catalyzed H3K27 acetylation at the FDFT1 locus, linking NeuroD1-driven histone acetylation to cholesterol biosynthesis in HCC. ChIP assay (NeuroD1 binding to FDFT1 promoter), Western blot, RT-qPCR, KAT2A activity assays, loss-of-function/overexpression experiments Oncogene Medium 40890513
2025 THEM6 stabilizes FDFT1 protein by interacting with HSP90 to protect FDFT1 from K48-linked ubiquitination and endoplasmic reticulum-associated degradation (ERAD), thereby prolonging FDFT1 protein half-life and increasing intracellular cholesterol biosynthesis; elevated cholesterol from this mechanism decreases ferroptosis susceptibility in TNBC cells. Co-immunoprecipitation (THEM6-HSP90, FDFT1 ubiquitination), Western blot, protein half-life analysis, siRNA knockdown, overexpression, in vitro and in vivo (xenograft) functional assays, ferroptosis markers (GPX4, SLC7A11, ACSL4, ROS, MDA) Oncogene High 40931051
2025 FDFT1 acts as a negative regulator of autophagy in HCC cells; loss of FDFT1 increased autophagosome formation and lysosomal fusion, while FDFT1 overexpression suppressed basal and induced autophagy through AMPK-ULK1 signaling. siRNA knockdown, overexpression, autophagosome imaging, Western blot for AMPK-ULK1 pathway markers Biomolecules & therapeutics Medium 42059033
2025 In colorectal cancer, atorvastatin activates the SREBP2-FDFT1 axis (by depleting cellular cholesterol via HMGCR inhibition), and FDFT1-mediated inhibition of the PI3K/AKT pathway induces ER stress, autophagy, and ferroptosis to promote lipid catabolism. In vivo AOM/DSS CRC mouse model, Western blot, pathway analysis, FDFT1 overexpression/knockdown Cell communication and signaling Medium 41866501
2024 In chicken theca cells, estrogen promotes FDFT1 expression via GSK3β phosphorylation at Tyr216, which enhances binding of GSK3β to LSD1, increasing LSD1Ser54 phosphorylation; elevated LSD1Ser54p then activates FDFT1 transcription, promoting cholesterol biosynthesis. CUT&RUN sequencing, transcriptome sequencing, overexpression/knockdown, Western blot, co-immunoprecipitation (GSK3β-LSD1), RT-qPCR Biomolecules Medium 39595520
2025 HIV-1 Tat downregulates FDFT1 expression in BCBL-1 cells, reducing cellular cholesterol levels; FDFT1 knockdown upregulates KSHV lytic reactivation genes (ORF50) while FDFT1 overexpression upregulates latency gene (ORF73), establishing FDFT1-mediated cholesterol regulation as a modulator of KSHV replication state. Lentiviral overexpression/RNAi knockdown, RT-qPCR, cholesterol assay Current HIV research Low 40947702
2025 piR-39980 targets FDFT1, and suppression of FDFT1 leads to inhibition of CYPOR and the EIF3H/HIF1α axis; CYPOR inhibition increases doxorubicin accumulation, and EIF3H/HIF1α axis inhibition induces DNA break-mediated apoptosis, thereby enhancing doxorubicin sensitivity in tongue cancer cells. Dual luciferase assay, Western blot, RT-qPCR, flow cytometry, migration assays, molecular assays for CYPOR and HIF1α Archives of biochemistry and biophysics Medium 40339976
2025 Squalene synthase (SQS/FDFT1) inhibition in lung cancer cells using pharmacological inhibitors suppressed tumor growth in vivo and reduced lung inflammation and tumor burden, providing evidence that SQS is a functionally important enzyme target in lung cancer. In vitro cancer cell assays with SQS inhibitors, in vivo tumor burden and lung inflammation models ACS medicinal chemistry letters Medium 41089479
2025 METTL7A directly binds SREBP1 and SCAP, hindering nuclear translocation of SREBP1, thereby reducing expression of FDFT1 (and other cholesterol synthesis genes SQLE, CYP51A1) and intracellular cholesterol content in colorectal cancer cells. Co-immunoprecipitation (METTL7A-SREBP1, METTL7A-SCAP), Western blot, immunofluorescence, transcriptomics, proteomics, in vitro and in vivo functional assays Cellular oncology Medium 42009961

Source papers

Stage 0 corpus · 44 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2020 Fasting inhibits aerobic glycolysis and proliferation in colorectal cancer via the Fdft1-mediated AKT/mTOR/HIF1α pathway suppression. Nature communications 219 32313017
2007 Cloning and characterization of squalene synthase (SQS) gene from Ganoderma lucidum. Journal of microbiology and biotechnology 54 18051320
2020 Bavachinin inhibits cholesterol synthesis enzyme FDFT1 expression via AKT/mTOR/SREBP-2 pathway. International immunopharmacology 36 32827918
1994 Localization of the squalene synthase gene (FDFT1) to human chromosome 8p22-p23.1. Genomics 27 8020937
2018 Characterization of farnesyl diphosphate farnesyl transferase 1 (FDFT1) expression in cancer. Personalized medicine 25 30468409
2022 Identification of FDFT1 as a potential biomarker associated with ferroptosis in ccRCC. Cancer medicine 24 35322581
2022 Raman spectroscopy biochemical characterisation of bladder cancer cisplatin resistance regulated by FDFT1: a review. Cellular & molecular biology letters 23 35093030
2020 20(S)-Rg3 upregulates FDFT1 via reducing miR-4425 to inhibit ovarian cancer progression. Archives of biochemistry and biophysics 22 32877662
2019 Dual Regulatory Mechanisms of Expression and Mutation Involving Metabolism-Related Genes FDFT1 and UQCR5 during CLM. Molecular therapy oncolytics 21 31236441
2025 Targeting FDFT1 Reduces Cholesterol and Bile Acid Production and Delays Hepatocellular Carcinoma Progression Through the HNF4A/ALDOB/AKT1 Axis. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 20 39899681
2023 FDFT1 repression by piR-39980 prevents oncogenesis by regulating proliferation and apoptosis through hypoxia in tongue squamous cell carcinoma. Life sciences 19 37473805
2013 Role of FDFT1 polymorphism for fibrosis progression in patients with chronic hepatitis C. Liver international : official journal of the International Association for the Study of the Liver 18 23870067
2024 Gene-specific somatic epigenetic mosaicism of FDFT1 underlies a non-hereditary localized form of porokeratosis. American journal of human genetics 17 38653249
2018 Cloning, Expression Analysis and Functional Characterization of Squalene Synthase (SQS) from Tripterygium wilfordii. Molecules (Basel, Switzerland) 16 29382150
2015 Cloning, prokaryotic expression and functional analysis of squalene synthase (SQS) in Magnolia officinalis. Protein expression and purification 15 26696600
2024 Artemisitene induces apoptosis of breast cancer cells by targeting FDFT1 and inhibits the growth of breast cancer patient-derived organoids. Phytomedicine : international journal of phytotherapy and phytopharmacology 12 39461203
2009 Studies of CTNNBL1 and FDFT1 variants and measures of obesity: analyses of quantitative traits and case-control studies in 18,014 Danes. BMC medical genetics 12 19245693
2023 3β-Hydroxy-12-oleanen-27-oic Acid Exerts an Antiproliferative Effect on Human Colon Carcinoma HCT116 Cells via Targeting FDFT1. International journal of molecular sciences 9 37834468
2016 Sequential simulation (SqS) of clinical pathways: a tool for public and patient engagement in point-of-care diagnostics. BMJ open 9 27625053
2024 FDFT1 maintains glioblastoma stem cells through activation of the Akt pathway. Stem cell research & therapy 8 39707501
2023 The Identification of SQS/SQE/OSC Gene Families in Regulating the Biosynthesis of Triterpenes in Potentilla anserina. Molecules (Basel, Switzerland) 7 36985754
2025 NeuroD1 drives a KAT2A-FDFT1 signaling axis to promote cholesterol biosynthesis and hepatocellular carcinoma progression via histone H3K27 acetylation. Oncogene 6 40890513
2020 Protective mechanism of fdft1 in steroid hormone synthesis pathway in SD rats with acute hypoxic injury. Genes & genomics 6 32980992
2007 Functional polymorphisms of the Lss and Fdft1 genes in laboratory rats. Experimental animals 6 17460354
2025 Disrupted Lipid Metabolism Aggravates Ischemic Brain Injury: Targeting FDFT1 for Stroke Therapy. Molecular neurobiology 5 40676368
2022 cDNA cloning, prokaryotic expression, and functional analysis of squalene synthase (SQS) in Camellia vietnamensis Huang. Protein expression and purification 5 35272013
2011 Exclusion of CTSB and FDFT1 as positional and functional candidate genes for keratolytic winter erythema (KWE). Journal of dermatological science 5 21945151
2025 Valproic acid induces ferroptosis and suppresses the proliferation of MDA-MB-231 cells by targeting FDFT1. Frontiers in pharmacology 4 40438588
2025 THEM6 modulates carboplatin sensitivity by regulating ferroptosis through FDFT1 in triple-negative breast cancer. Breast cancer research : BCR 4 40619388
2024 MicroRNA-146b-5p/FDFT1 mediates cisplatin sensitivity in bladder cancer by redirecting cholesterol biosynthesis to the non-sterol branch. The international journal of biochemistry & cell biology 4 39270927
2025 Identification of FDFT1 and PGRMC1 as New Biomarkers in Nonalcoholic Steatohepatitis (NASH)-Related Hepatocellular Carcinoma by Deep Learning. Journal of hepatocellular carcinoma 3 40206734
2025 A piRNA chemosensitizes doxorubicin in tongue squamous cell carcinoma by targeting FDFT1 and inhibiting the EIF3H/HIF1α/CYPOR axis. Archives of biochemistry and biophysics 3 40339976
2024 Estrogen Enhances FDFT1 Expression in Theca Cells of Chicken Hierarchical Ovarian Follicles by Increasing LSD1Ser54p Level Through GSK3β Phosphorylation at 216th Tyrosine. Biomolecules 3 39595520
2025 EMC2 promotes triple negative breast cancer growth by protecting FDFT1 from endoplasmic reticulum associated degradation to impair ferroptosis susceptibility. Oncogene 2 40931051
2025 Impact of HIV-1 Tat on FDFT1 Suppression, Changes in Cholesterol Level, and KSHV Replication in BCBL1 Cells. Current HIV research 2 40947702
2024 Spectroscopic diagnosis and metabolite characterization of cisplatin resistance regulated by FDFT1 in bladder cancer tissue. Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine 2 38810354
2009 [Culture of transgenic Glycyrrhiza uralensis hairy root with licorice squalene synthase (SQS) gene]. Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica 2 19894527
2022 FDFT1/FGFR2 rearrangement: A newly identified anlotinib-sensitive FGFR2 variant in cholangiocarcinoma. Cancer treatment and research communications 1 35477128
2026 Atorvastatin promotes lipid catabolism in colorectal cancer via FDFT1‒mediated inhibition of the PI3K/AKT pathway. Cell communication and signaling : CCS 0 41866501
2026 METTL7A inhibits progression of colorectal cancer through the SREBP1 / FDFT1 / SQLE / CYP51A1 / cholesterol metabolic pathway. Cellular oncology (Dordrecht, Netherlands) 0 42009961
2025 Discovery of an SQS-PSY Domain-Containing Protein in Meloidogyne incognita Reveals Its Function in Parasitism. International journal of molecular sciences 0 41009671
2025 Unraveling the Potential Pathogenic Role of Squalene Synthase (SQS) in Lung Cancer Using Enzyme Inhibitors as Molecular Tools. ACS medicinal chemistry letters 0 41089479
2025 FDFT1 Acts as a Negative Regulator of Autophagy by Modulating AMPK-ULK1 Signaling in Hepatocellular Carcinoma Cells. Biomolecules & therapeutics 0 42059033
2018 Optimizing special quasirandom structure (SQS) models for accurate functional property prediction in disordered 2D alloys. Journal of physics. Condensed matter : an Institute of Physics journal 0 30406769

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