{"gene":"FADS3","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2013,"finding":"Rat FADS3 catalyzes Δ13-desaturation of trans-vaccenate (vaccenic acid) to produce a Δ11,13-conjugated linoleic acid (CLA) isomer strongly consistent with trans11,cis13-CLA, representing the first 'methyl-end' fatty acid desaturase functionally characterized in mammals. FADS3 does not display Δ5-, Δ6-, or Δ9-desaturase activity. Knockdown of FADS3 in rat hepatocytes specifically reduces trans-vaccenate Δ13-desaturation.","method":"In vitro desaturase activity assay with rat FADS3, structural characterization of product, siRNA knockdown in rat hepatocytes with fatty acid profiling","journal":"Journal of lipid research","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro enzymatic activity assay plus cell-based knockdown with specific lipid phenotype, replicated in subsequent studies","pmids":["24070791"],"is_preprint":false},{"year":2016,"finding":"Bovine mammary MAC-T and BME-UV epithelial cells express FADS3 mRNA and synthesize trans-11,cis-13 CLA from vaccenic acid, consistent with FADS3-catalyzed Δ13-desaturation of vaccenic acid occurring in mammary tissue, extending the finding beyond rodents to ruminant species.","method":"Cell-based incubation of bovine mammary epithelial cells with vaccenic acid; RT-PCR for FADS3 expression; structural comparison of product to rodent FADS3-derived CLA","journal":"Journal of dairy science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-based assay with structural characterization, single lab, multiple lines of evidence across cell types and tissues","pmids":["27865506"],"is_preprint":false},{"year":2019,"finding":"FADS3 is a bona fide Δ14Z long-chain base (LCB) desaturase that introduces the Δ14Z double bond into sphingosine to produce sphingadienine (d18:2). FADS3 is also required for conversion of cytotoxic 1-deoxysphinganine (m18:0) to 1-deoxysphingosine (m18:1). FADS3-overexpressing HEK293 cells are more resistant to m18:0 toxicity than wild-type cells.","method":"Metabolic labeling assays, FADS3 overexpression and knockdown in cell lines, plasma LCB profiling in FADS3-deficient mice, GWAS association with d18:2/d18:1 ratio","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (overexpression, knockdown, KO mouse metabolic profiling, metabolic labeling), functional rescue experiment","pmids":["31862735"],"is_preprint":false},{"year":2020,"finding":"FADS3 acts as a ceramide desaturase that produces 4,14-sphingadiene (SPD) ceramides by desaturating ceramides containing sphingosine (introducing the cis Δ14 double bond). SPD sphingolipids are preferentially localized outside lipid microdomains.","method":"Biochemical identification of FADS3 as ceramide desaturase; lipid microdomain fractionation showing localization of SPD sphingolipids outside microdomains","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — enzymatic activity established in cells, substrate identification, lipid microdomain fractionation, consistent with concurrent independent study (PMID:31862735)","pmids":["31916624"],"is_preprint":false},{"year":2023,"finding":"FADS3 is active toward sphingosine-containing ceramides (SPH-CERs) but NOT toward free sphingosine, establishing ceramide as the obligate substrate. FADS3 shows chain-length specificity for the sphingosine moiety (active on C16-C20 SPH-CERs) but not for the fatty acid moiety. FADS3 uses NADH or NADPH as electron donor, with cytochrome b5 facilitating electron transfer. Metabolic flow from SPD proceeds preferentially to sphingomyelin over glycosphingolipids.","method":"Cell-based assay using ceramide synthase inhibitor, in vitro enzymatic assay with defined substrates, cofactor requirement analysis","journal":"Biochimica et biophysica acta. Molecular and cell biology of lipids","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assay plus cell-based assay with substrate/cofactor specificity profiling, single lab but multiple orthogonal approaches","pmids":["37209771"],"is_preprint":false},{"year":2017,"finding":"Fads3 knockout (KO) mice show lower DHA (22:6n-3) levels in postnatal day 1 brain and a higher DPA/DHA ratio in liver, suggesting Fads3 enhances liver-mediated 22:6n-3 synthesis to support brain DHA accretion. KO mice also show lower 20:4n-6 but higher 22:4n-6 in liver. Fads1 and Fads2 mRNA levels are downregulated and Elovl2/Elovl5 upregulated in KO liver. No Δ13-desaturation of vaccenic acid was detected in liver or heart of WT mice expressing FADS3 in vivo.","method":"Fads3 knockout mouse generation, fatty acid profiling by gas chromatography, qRT-PCR for related gene expression","journal":"Prostaglandins, leukotrienes, and essential fatty acids","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with lipid phenotyping and gene expression analysis, single lab, in vivo model","pmids":["28838557"],"is_preprint":false},{"year":2017,"finding":"Fads3 knockout mice show no Δ13-desaturation of vaccenic acid in liver or heart in vivo (negative result in contrast to the in vitro activity reported earlier), suggesting the Δ13-desaturation activity toward vaccenic acid may not operate in liver or heart under physiological conditions.","method":"Fads3 knockout mouse, fatty acid profiling, vaccenic acid tracking in liver and heart","journal":"Prostaglandins, leukotrienes, and essential fatty acids","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — KO mouse with negative result, single lab, single in vivo study; contradicts in vitro Tier 1 findings","pmids":["28838557"],"is_preprint":false},{"year":2012,"finding":"FADS3 alternative transcripts are upregulated by dietary long-chain polyunsaturated fatty acids (DHA or ARA) in baboon neonatal liver and in HepG2 cells via a PPARγ-dependent mechanism, distinct from the regulation of FADS1 and FADS2 (which are downregulated). The PPARγ antagonist GW9662 prevents FADS3 upregulation.","method":"qRT-PCR of baboon neonate liver after dietary LCPUFA intervention; HepG2 cell treatment with DHA/ARA and PPARγ antagonist GW9662","journal":"Prostaglandins, leukotrienes, and essential fatty acids","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo dietary intervention plus pharmacological inhibition in cell line, two orthogonal systems, single lab","pmids":["22398025"],"is_preprint":false},{"year":2014,"finding":"The 51 kDa FADS3 isoform in rat hepatocytes localizes to the cytosolic fraction and is secreted into the extracellular matrix on fibronectin-containing fibers via exosome-like vesicles; FADS3 is also detected in serum. This localization is distinct from Δ5- and Δ6-desaturases.","method":"Subcellular fractionation, immunofluorescence/confocal imaging, exosome characterization, serum immunodetection in rat hepatocytes","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — direct fractionation and imaging showing novel extracellular localization, single lab, no functional consequence established","pmids":["23966218"],"is_preprint":false},{"year":2009,"finding":"Multiple FADS3 protein isoforms (75 kDa, 51 kDa, 37 kDa) exist in rat and mouse tissues in a tissue-dependent manner, detectable by specific polyclonal antibodies against N- and C-terminal ends, and additional isoforms are present in human cells and tissues.","method":"Western blotting with isoform-specific polyclonal antibodies in rat, mouse, and human tissues; qRT-PCR for mRNA levels","journal":"Journal of lipid research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — antibody-based detection replicated across species and tissues, single lab","pmids":["19752397"],"is_preprint":false},{"year":2025,"finding":"In ccRCC cells, FADS3 activates Smad2/3 phosphorylation through autocrine TGF-β signaling. FADS3-induced lipid droplets act as a reservoir of acetyl-CoA, promoting Smad2 acetylation and upregulation of TGF-β receptors, thereby promoting cell proliferation and EMT. FADS3 interaction partners were identified by co-immunoprecipitation and mass spectrometry.","method":"Co-immunoprecipitation, mass spectrometry, in vivo/in vitro cell proliferation and EMT assays, Smad2/3 phosphorylation and acetylation biochemical assays","journal":"International journal of surgery (London, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — co-IP/MS plus functional assays, single lab, single study, no independent replication","pmids":["41314810"],"is_preprint":false}],"current_model":"FADS3 is a multifunctional membrane-bound desaturase: it acts as a ceramide Δ14Z-desaturase that converts sphingosine-containing ceramides (not free sphingosine) into 4,14-sphingadienine ceramides using NADH/NADPH with cytochrome b5 as electron carrier, and also catalyzes Δ13-desaturation of trans-vaccenic acid to produce a trans11,cis13-CLA isomer in vitro and in mammary tissue; additionally, FADS3 alternative transcripts are regulated by PPARγ in response to dietary PUFA, multiple protein isoforms with distinct subcellular localizations (including extracellular secretion) exist in a tissue-dependent manner, and in cancer contexts FADS3 promotes EMT via autocrine TGF-β/Smad2/3 signaling linked to lipid droplet-derived acetyl-CoA."},"narrative":{"mechanistic_narrative":"FADS3 is a membrane-bound desaturase whose best-established physiological function is as a sphingolipid Δ14Z-desaturase that introduces a cis double bond into the long-chain base of ceramides to generate 4,14-sphingadiene (sphingadienine) sphingolipids [PMID:31862735, PMID:31916624]. Its obligate substrate is sphingosine-containing ceramide rather than free sphingosine, with selectivity for C16–C20 sphingosine moieties but not the N-acyl chain; catalysis uses NADH or NADPH with cytochrome b5 as the electron carrier, and the resulting sphingadiene flux is directed preferentially into sphingomyelin and away from lipid microdomains [PMID:31916624, PMID:37209771]. Through this activity FADS3 also detoxifies the cytotoxic atypical base 1-deoxysphinganine by desaturating it to 1-deoxysphingosine, conferring resistance to deoxysphingolipid toxicity [PMID:31862735]. FADS3 was originally characterized as a fatty acid Δ13-desaturase that converts trans-vaccenic acid to a trans11,cis13-conjugated linoleic acid isomer in vitro and in mammary epithelial cells [PMID:24070791, PMID:27865506], although this activity was not detectable in liver or heart of knockout mice, indicating it does not operate in those tissues under physiological conditions [PMID:28838557]. At the organismal level, Fads3 supports brain DHA accretion via liver n-3 PUFA synthesis [PMID:28838557], and its alternative transcripts are induced by dietary long-chain PUFA through a PPARγ-dependent mechanism distinct from FADS1/FADS2 [PMID:22398025]. In clear-cell renal cell carcinoma, FADS3 drives proliferation and EMT by generating lipid-droplet-derived acetyl-CoA that fuels Smad2 acetylation and autocrine TGF-β/Smad2/3 signaling [PMID:41314810].","teleology":[{"year":2009,"claim":"Before any catalytic role was defined, it was unknown whether FADS3 was expressed as a single product; demonstrating multiple tissue-dependent protein isoforms established FADS3 as a structurally complex gene with potential for distinct functional forms.","evidence":"Isoform-specific polyclonal antibody Western blotting and qRT-PCR across rat, mouse, and human tissues","pmids":["19752397"],"confidence":"Medium","gaps":["Functional differences between isoforms not defined","Catalytic identity of isoforms unknown at this stage"]},{"year":2012,"claim":"The regulatory logic of FADS3 was unknown; showing dietary PUFA induce FADS3 alternative transcripts via PPARγ placed FADS3 in a regulatory regime opposite to that of FADS1/FADS2.","evidence":"Dietary LCPUFA intervention in baboon neonate liver and HepG2 cells with PPARγ antagonist GW9662","pmids":["22398025"],"confidence":"Medium","gaps":["Direct PPARγ binding to FADS3 regulatory elements not demonstrated","Functional consequence of transcript induction not measured"]},{"year":2013,"claim":"FADS3 had no assigned enzymatic activity; in vitro desaturation of trans-vaccenate to a trans11,cis13-CLA isomer provided the first functional characterization of a mammalian methyl-end fatty acid desaturase.","evidence":"In vitro desaturase activity assay with rat FADS3, product structural characterization, and siRNA knockdown in rat hepatocytes","pmids":["24070791"],"confidence":"High","gaps":["Physiological relevance in vivo not established","Electron donor and cofactor requirements not defined here"]},{"year":2014,"claim":"The subcellular behavior of FADS3 was unknown; finding that the 51 kDa isoform is cytosolic, secreted on fibronectin fibers via exosome-like vesicles, and present in serum revealed an unexpected extracellular distribution distinct from other desaturases.","evidence":"Subcellular fractionation, confocal imaging, exosome characterization, and serum immunodetection in rat hepatocytes","pmids":["23966218"],"confidence":"Medium","gaps":["Functional role of secreted FADS3 not established","Mechanism of secretion not defined"]},{"year":2017,"claim":"Whether FADS3 contributes to PUFA homeostasis in vivo was unclear; knockout mice revealed altered DHA/DPA balance supporting brain DHA accretion, while showing the in vitro Δ13-CLA activity does not operate in liver or heart.","evidence":"Fads3 knockout mouse fatty acid profiling by gas chromatography and qRT-PCR of related genes","pmids":["28838557"],"confidence":"Medium","gaps":["Mechanism by which Fads3 loss alters DHA synthesis unresolved","Tissue context where Δ13-desaturation operates not identified","Negative in vivo result conflicts with in vitro activity"]},{"year":2020,"claim":"The principal physiological substrate of FADS3 was redefined; identification as a Δ14Z long-chain base and ceramide desaturase producing sphingadiene sphingolipids established a sphingolipid rather than fatty-acid-centric role, and linked FADS3 to detoxification of 1-deoxysphinganine.","evidence":"Metabolic labeling, overexpression/knockdown, KO mouse LCB profiling, GWAS association, and biochemical ceramide desaturase identification with microdomain fractionation","pmids":["31862735","31916624"],"confidence":"High","gaps":["Structural basis of substrate selectivity not resolved","Cofactor requirements not yet defined"]},{"year":2023,"claim":"The enzymatic mechanism was incompletely defined; establishing that ceramide (not free sphingosine) is the obligate substrate, with chain-length specificity for the sphingosine moiety and NADH/NADPH-cytochrome b5 cofactor dependence, completed the biochemical model and traced flux toward sphingomyelin.","evidence":"Cell-based assay with ceramide synthase inhibitor, in vitro enzymatic assay with defined substrates, and cofactor requirement analysis","pmids":["37209771"],"confidence":"High","gaps":["No structural model of the catalytic site","Regulation of substrate access not defined"]},{"year":2025,"claim":"A role in disease was unknown; in ccRCC FADS3 was shown to drive proliferation and EMT through lipid-droplet-derived acetyl-CoA promoting Smad2 acetylation and autocrine TGF-β/Smad2/3 signaling.","evidence":"Co-immunoprecipitation, mass spectrometry, proliferation/EMT assays, and Smad2/3 phosphorylation/acetylation biochemistry","pmids":["41314810"],"confidence":"Medium","gaps":["Link between desaturase activity and acetyl-CoA generation not mechanistically resolved","Single study without independent replication","Direct FADS3 interaction partners not validated reciprocally"]},{"year":null,"claim":"It remains unresolved how FADS3 sphingolipid desaturase activity, the tissue-restricted fatty acid Δ13-desaturase activity, and the secreted/oncogenic functions are mechanistically connected within a single protein, and whether distinct isoforms underlie these distinct activities.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model linking activities","Isoform-specific function not mapped to catalytic roles","Physiological substrate hierarchy across tissues unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016491","term_label":"oxidoreductase activity","supporting_discovery_ids":[0,2,3,4]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[2,3,4]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[8]},{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[8]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,2,3,4,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[10]}],"complexes":[],"partners":["CYB5A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y5Q0","full_name":"Fatty acid desaturase 3","aliases":["Delta(13) fatty acid desaturase","Delta(13) desaturase"],"length_aa":445,"mass_kda":51.1,"function":"Mammals have different sphingoid bases that differ in their length and/or pattern of desaturation and hydroxyl groups. The predominant sphingoid base that comprises mammalian ceramides is sphing-4-enine (sphingosine or SPH) which has a trans (E) desaturation at carbon 4 (PubMed:31862735, PubMed:31916624). FADS3 is a desaturase that introduces a cis (Z) double bond between carbon 14 and carbon 15 of the sphingoid base (also known as long chain base, LCB), producing LCBs such as sphinga-4,14-dienine (SPD, d18:2(4E,14Z)) from SPH (PubMed:31862735, PubMed:31916624, PubMed:37209771). Prefers SPH-containing ceramides (N-acylsphing-4-enines) as substrates (PubMed:31862735, PubMed:31916624, PubMed:37209771). Capable of metabolizing also the SPH in its free form (PubMed:31862735). SPD ceramides occur widely in mammalian tissues and cells (PubMed:31916624). Due to their unusual structure containing a cis double bond, SPD ceramides may have an opposite, negative role in lipid microdomain formation relative to conventional ceramides (PubMed:31916624). Could be involved in the detoxification of 1-deoxy sphingolipids, by desaturating the cytotoxic 1-deoxysphinganine (1-deoxySA, m18:0), produced under pathological conditions, to 1-deoxysphingenine (1-deoxysphingosine, 1-deoxySO, m18:1) (Probable). Although prefers SPH-containing ceramides (N-acylsphing-4-enines) as substrates, it also exhibits activity toward dihydrosphingosine-containing CERs (N-acylsphinganines) and produces 14Z-SPH-containing sphingolipids,which can be found in patients with DEGS1 mutations (PubMed:37209771). Its desaturase mechanism involves an electron transfer facilitated by cytochrome b5 (PubMed:37209771). FADS3 also acts as a methyl-end fatty acyl coenzyme A (CoA) desaturase that introduces a cis double bond between the preexisting double bond and the terminal methyl group of the fatty acyl chain (By similarity). Desaturates (11E)-octadecenoate (trans-vaccenoate, the predominant trans fatty acid in human milk) at carbon 13 to generate (11E,13Z)-octadecadienoate (also known as conjugated linoleic acid 11E,13Z-CLA) (By similarity)","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/Q9Y5Q0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FADS3","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FADS3","total_profiled":1310},"omim":[{"mim_id":"618389","title":"FETAL AKINESIA DEFORMATION SEQUENCE 3; FADS3","url":"https://www.omim.org/entry/618389"},{"mim_id":"612795","title":"POLYUNSATURATED FATTY ACIDS PLASMA LEVEL QUANTITATIVE TRAIT LOCUS 1; PUFAQTL1","url":"https://www.omim.org/entry/612795"},{"mim_id":"610285","title":"DOWNSTREAM OF TYROSINE KINASE 7; DOK7","url":"https://www.omim.org/entry/610285"},{"mim_id":"606150","title":"FATTY ACID DESATURASE 3; FADS3","url":"https://www.omim.org/entry/606150"},{"mim_id":"606149","title":"FATTY ACID DESATURASE 2; FADS2","url":"https://www.omim.org/entry/606149"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli fibrillar center","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FADS3"},"hgnc":{"alias_symbol":["CYB5RP"],"prev_symbol":["LLCDL3"]},"alphafold":{"accession":"Q9Y5Q0","domains":[{"cath_id":"3.10.120.10","chopping":"11-94","consensus_level":"medium","plddt":89.4317,"start":11,"end":94},{"cath_id":"-","chopping":"105-445","consensus_level":"medium","plddt":96.7944,"start":105,"end":445}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5Q0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5Q0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5Q0-F1-predicted_aligned_error_v6.png","plddt_mean":93.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FADS3","jax_strain_url":"https://www.jax.org/strain/search?query=FADS3"},"sequence":{"accession":"Q9Y5Q0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y5Q0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y5Q0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5Q0"}},"corpus_meta":[{"pmid":"19750004","id":"PMC_19750004","title":"A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia.","date":"2009","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19750004","citation_count":126,"is_preprint":false},{"pmid":"31862735","id":"PMC_31862735","title":"FADS3 is a Δ14Z sphingoid base desaturase that contributes to gender differences in the human plasma sphingolipidome.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31862735","citation_count":75,"is_preprint":false},{"pmid":"22398025","id":"PMC_22398025","title":"Dietary long-chain polyunsaturated fatty acids upregulate expression of FADS3 transcripts.","date":"2012","source":"Prostaglandins, leukotrienes, and essential fatty acids","url":"https://pubmed.ncbi.nlm.nih.gov/22398025","citation_count":46,"is_preprint":false},{"pmid":"31916624","id":"PMC_31916624","title":"Biosynthesis of the anti-lipid-microdomain sphingoid base 4,14-sphingadiene by the ceramide desaturase FADS3.","date":"2020","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/31916624","citation_count":41,"is_preprint":false},{"pmid":"19573581","id":"PMC_19573581","title":"Novel fatty acid desaturase 3 (FADS3) transcripts generated by alternative splicing.","date":"2009","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/19573581","citation_count":40,"is_preprint":false},{"pmid":"19752397","id":"PMC_19752397","title":"The fatty acid desaturase 3 gene encodes for different FADS3 protein isoforms in mammalian tissues.","date":"2009","source":"Journal of lipid research","url":"https://pubmed.ncbi.nlm.nih.gov/19752397","citation_count":39,"is_preprint":false},{"pmid":"20226833","id":"PMC_20226833","title":"Fatty Acid Desaturase 3 (Fads3) is a singular member of the Fads cluster.","date":"2010","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/20226833","citation_count":30,"is_preprint":false},{"pmid":"28838557","id":"PMC_28838557","title":"Fads3 modulates docosahexaenoic acid in liver and brain.","date":"2017","source":"Prostaglandins, leukotrienes, and essential fatty acids","url":"https://pubmed.ncbi.nlm.nih.gov/28838557","citation_count":27,"is_preprint":false},{"pmid":"24070791","id":"PMC_24070791","title":"Trans-vaccenate is Δ13-desaturated by FADS3 in rodents.","date":"2013","source":"Journal of lipid research","url":"https://pubmed.ncbi.nlm.nih.gov/24070791","citation_count":27,"is_preprint":false},{"pmid":"27865506","id":"PMC_27865506","title":"Synthesis of the suspected trans-11,cis-13 conjugated linoleic acid isomer in ruminant mammary tissue by FADS3-catalyzed Δ13-desaturation of vaccenic acid.","date":"2016","source":"Journal of dairy science","url":"https://pubmed.ncbi.nlm.nih.gov/27865506","citation_count":13,"is_preprint":false},{"pmid":"37209771","id":"PMC_37209771","title":"Metabolism of sphingadiene and characterization of the sphingadiene-producing enzyme FADS3.","date":"2023","source":"Biochimica et biophysica acta. Molecular and cell biology of lipids","url":"https://pubmed.ncbi.nlm.nih.gov/37209771","citation_count":11,"is_preprint":false},{"pmid":"27216536","id":"PMC_27216536","title":"Alternative splicing generates novel Fads3 transcript in mice.","date":"2016","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/27216536","citation_count":6,"is_preprint":false},{"pmid":"28161285","id":"PMC_28161285","title":"Genetic polymorphisms of FADS1, FADS2, and FADS3 and fatty acid profiles in subjects received methadone maintenance therapy.","date":"2017","source":"Prostaglandins, leukotrienes, and essential fatty acids","url":"https://pubmed.ncbi.nlm.nih.gov/28161285","citation_count":5,"is_preprint":false},{"pmid":"32911476","id":"PMC_32911476","title":"Fatty Acid Desaturase 3 (FADS3) Is a Specific ∆13-Desaturase of Ruminant trans-Vaccenic Acid.","date":"2019","source":"Lifestyle genomics","url":"https://pubmed.ncbi.nlm.nih.gov/32911476","citation_count":3,"is_preprint":false},{"pmid":"23966218","id":"PMC_23966218","title":"The 51 kDa FADS3 is secreted in the ECM of hepatocytes and blood in rat.","date":"2014","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23966218","citation_count":2,"is_preprint":false},{"pmid":"36364938","id":"PMC_36364938","title":"Novel Interactions of Myristic Acid and FADS3 Variants Predict Atopic Dermatitis among Indonesian Infants.","date":"2022","source":"Nutrients","url":"https://pubmed.ncbi.nlm.nih.gov/36364938","citation_count":2,"is_preprint":false},{"pmid":"41314810","id":"PMC_41314810","title":"FADS3 fuels CcRCC progression via lipid-droplet/TGF-β receptors axis bridging metabolic reprogramming and epithelial plasticity.","date":"2025","source":"International journal of surgery (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/41314810","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10788,"output_tokens":3139,"usd":0.039725,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10515,"output_tokens":3242,"usd":0.066812,"stage2_stop_reason":"end_turn"},"total_usd":0.106537,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"Rat FADS3 catalyzes Δ13-desaturation of trans-vaccenate (vaccenic acid) to produce a Δ11,13-conjugated linoleic acid (CLA) isomer strongly consistent with trans11,cis13-CLA, representing the first 'methyl-end' fatty acid desaturase functionally characterized in mammals. FADS3 does not display Δ5-, Δ6-, or Δ9-desaturase activity. Knockdown of FADS3 in rat hepatocytes specifically reduces trans-vaccenate Δ13-desaturation.\",\n      \"method\": \"In vitro desaturase activity assay with rat FADS3, structural characterization of product, siRNA knockdown in rat hepatocytes with fatty acid profiling\",\n      \"journal\": \"Journal of lipid research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro enzymatic activity assay plus cell-based knockdown with specific lipid phenotype, replicated in subsequent studies\",\n      \"pmids\": [\"24070791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Bovine mammary MAC-T and BME-UV epithelial cells express FADS3 mRNA and synthesize trans-11,cis-13 CLA from vaccenic acid, consistent with FADS3-catalyzed Δ13-desaturation of vaccenic acid occurring in mammary tissue, extending the finding beyond rodents to ruminant species.\",\n      \"method\": \"Cell-based incubation of bovine mammary epithelial cells with vaccenic acid; RT-PCR for FADS3 expression; structural comparison of product to rodent FADS3-derived CLA\",\n      \"journal\": \"Journal of dairy science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-based assay with structural characterization, single lab, multiple lines of evidence across cell types and tissues\",\n      \"pmids\": [\"27865506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FADS3 is a bona fide Δ14Z long-chain base (LCB) desaturase that introduces the Δ14Z double bond into sphingosine to produce sphingadienine (d18:2). FADS3 is also required for conversion of cytotoxic 1-deoxysphinganine (m18:0) to 1-deoxysphingosine (m18:1). FADS3-overexpressing HEK293 cells are more resistant to m18:0 toxicity than wild-type cells.\",\n      \"method\": \"Metabolic labeling assays, FADS3 overexpression and knockdown in cell lines, plasma LCB profiling in FADS3-deficient mice, GWAS association with d18:2/d18:1 ratio\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (overexpression, knockdown, KO mouse metabolic profiling, metabolic labeling), functional rescue experiment\",\n      \"pmids\": [\"31862735\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"FADS3 acts as a ceramide desaturase that produces 4,14-sphingadiene (SPD) ceramides by desaturating ceramides containing sphingosine (introducing the cis Δ14 double bond). SPD sphingolipids are preferentially localized outside lipid microdomains.\",\n      \"method\": \"Biochemical identification of FADS3 as ceramide desaturase; lipid microdomain fractionation showing localization of SPD sphingolipids outside microdomains\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — enzymatic activity established in cells, substrate identification, lipid microdomain fractionation, consistent with concurrent independent study (PMID:31862735)\",\n      \"pmids\": [\"31916624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FADS3 is active toward sphingosine-containing ceramides (SPH-CERs) but NOT toward free sphingosine, establishing ceramide as the obligate substrate. FADS3 shows chain-length specificity for the sphingosine moiety (active on C16-C20 SPH-CERs) but not for the fatty acid moiety. FADS3 uses NADH or NADPH as electron donor, with cytochrome b5 facilitating electron transfer. Metabolic flow from SPD proceeds preferentially to sphingomyelin over glycosphingolipids.\",\n      \"method\": \"Cell-based assay using ceramide synthase inhibitor, in vitro enzymatic assay with defined substrates, cofactor requirement analysis\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular and cell biology of lipids\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay plus cell-based assay with substrate/cofactor specificity profiling, single lab but multiple orthogonal approaches\",\n      \"pmids\": [\"37209771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Fads3 knockout (KO) mice show lower DHA (22:6n-3) levels in postnatal day 1 brain and a higher DPA/DHA ratio in liver, suggesting Fads3 enhances liver-mediated 22:6n-3 synthesis to support brain DHA accretion. KO mice also show lower 20:4n-6 but higher 22:4n-6 in liver. Fads1 and Fads2 mRNA levels are downregulated and Elovl2/Elovl5 upregulated in KO liver. No Δ13-desaturation of vaccenic acid was detected in liver or heart of WT mice expressing FADS3 in vivo.\",\n      \"method\": \"Fads3 knockout mouse generation, fatty acid profiling by gas chromatography, qRT-PCR for related gene expression\",\n      \"journal\": \"Prostaglandins, leukotrienes, and essential fatty acids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with lipid phenotyping and gene expression analysis, single lab, in vivo model\",\n      \"pmids\": [\"28838557\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Fads3 knockout mice show no Δ13-desaturation of vaccenic acid in liver or heart in vivo (negative result in contrast to the in vitro activity reported earlier), suggesting the Δ13-desaturation activity toward vaccenic acid may not operate in liver or heart under physiological conditions.\",\n      \"method\": \"Fads3 knockout mouse, fatty acid profiling, vaccenic acid tracking in liver and heart\",\n      \"journal\": \"Prostaglandins, leukotrienes, and essential fatty acids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — KO mouse with negative result, single lab, single in vivo study; contradicts in vitro Tier 1 findings\",\n      \"pmids\": [\"28838557\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FADS3 alternative transcripts are upregulated by dietary long-chain polyunsaturated fatty acids (DHA or ARA) in baboon neonatal liver and in HepG2 cells via a PPARγ-dependent mechanism, distinct from the regulation of FADS1 and FADS2 (which are downregulated). The PPARγ antagonist GW9662 prevents FADS3 upregulation.\",\n      \"method\": \"qRT-PCR of baboon neonate liver after dietary LCPUFA intervention; HepG2 cell treatment with DHA/ARA and PPARγ antagonist GW9662\",\n      \"journal\": \"Prostaglandins, leukotrienes, and essential fatty acids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo dietary intervention plus pharmacological inhibition in cell line, two orthogonal systems, single lab\",\n      \"pmids\": [\"22398025\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The 51 kDa FADS3 isoform in rat hepatocytes localizes to the cytosolic fraction and is secreted into the extracellular matrix on fibronectin-containing fibers via exosome-like vesicles; FADS3 is also detected in serum. This localization is distinct from Δ5- and Δ6-desaturases.\",\n      \"method\": \"Subcellular fractionation, immunofluorescence/confocal imaging, exosome characterization, serum immunodetection in rat hepatocytes\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — direct fractionation and imaging showing novel extracellular localization, single lab, no functional consequence established\",\n      \"pmids\": [\"23966218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Multiple FADS3 protein isoforms (75 kDa, 51 kDa, 37 kDa) exist in rat and mouse tissues in a tissue-dependent manner, detectable by specific polyclonal antibodies against N- and C-terminal ends, and additional isoforms are present in human cells and tissues.\",\n      \"method\": \"Western blotting with isoform-specific polyclonal antibodies in rat, mouse, and human tissues; qRT-PCR for mRNA levels\",\n      \"journal\": \"Journal of lipid research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — antibody-based detection replicated across species and tissues, single lab\",\n      \"pmids\": [\"19752397\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In ccRCC cells, FADS3 activates Smad2/3 phosphorylation through autocrine TGF-β signaling. FADS3-induced lipid droplets act as a reservoir of acetyl-CoA, promoting Smad2 acetylation and upregulation of TGF-β receptors, thereby promoting cell proliferation and EMT. FADS3 interaction partners were identified by co-immunoprecipitation and mass spectrometry.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, in vivo/in vitro cell proliferation and EMT assays, Smad2/3 phosphorylation and acetylation biochemical assays\",\n      \"journal\": \"International journal of surgery (London, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — co-IP/MS plus functional assays, single lab, single study, no independent replication\",\n      \"pmids\": [\"41314810\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FADS3 is a multifunctional membrane-bound desaturase: it acts as a ceramide Δ14Z-desaturase that converts sphingosine-containing ceramides (not free sphingosine) into 4,14-sphingadienine ceramides using NADH/NADPH with cytochrome b5 as electron carrier, and also catalyzes Δ13-desaturation of trans-vaccenic acid to produce a trans11,cis13-CLA isomer in vitro and in mammary tissue; additionally, FADS3 alternative transcripts are regulated by PPARγ in response to dietary PUFA, multiple protein isoforms with distinct subcellular localizations (including extracellular secretion) exist in a tissue-dependent manner, and in cancer contexts FADS3 promotes EMT via autocrine TGF-β/Smad2/3 signaling linked to lipid droplet-derived acetyl-CoA.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FADS3 is a membrane-bound desaturase whose best-established physiological function is as a sphingolipid \\u039414Z-desaturase that introduces a cis double bond into the long-chain base of ceramides to generate 4,14-sphingadiene (sphingadienine) sphingolipids [#2, #3]. Its obligate substrate is sphingosine-containing ceramide rather than free sphingosine, with selectivity for C16\\u2013C20 sphingosine moieties but not the N-acyl chain; catalysis uses NADH or NADPH with cytochrome b5 as the electron carrier, and the resulting sphingadiene flux is directed preferentially into sphingomyelin and away from lipid microdomains [#3, #4]. Through this activity FADS3 also detoxifies the cytotoxic atypical base 1-deoxysphinganine by desaturating it to 1-deoxysphingosine, conferring resistance to deoxysphingolipid toxicity [#2]. FADS3 was originally characterized as a fatty acid \\u039413-desaturase that converts trans-vaccenic acid to a trans11,cis13-conjugated linoleic acid isomer in vitro and in mammary epithelial cells [#0, #1], although this activity was not detectable in liver or heart of knockout mice, indicating it does not operate in those tissues under physiological conditions [#6]. At the organismal level, Fads3 supports brain DHA accretion via liver n-3 PUFA synthesis [#5], and its alternative transcripts are induced by dietary long-chain PUFA through a PPAR\\u03b3-dependent mechanism distinct from FADS1/FADS2 [#7]. In clear-cell renal cell carcinoma, FADS3 drives proliferation and EMT by generating lipid-droplet-derived acetyl-CoA that fuels Smad2 acetylation and autocrine TGF-\\u03b2/Smad2/3 signaling [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Before any catalytic role was defined, it was unknown whether FADS3 was expressed as a single product; demonstrating multiple tissue-dependent protein isoforms established FADS3 as a structurally complex gene with potential for distinct functional forms.\",\n      \"evidence\": \"Isoform-specific polyclonal antibody Western blotting and qRT-PCR across rat, mouse, and human tissues\",\n      \"pmids\": [\"19752397\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional differences between isoforms not defined\", \"Catalytic identity of isoforms unknown at this stage\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"The regulatory logic of FADS3 was unknown; showing dietary PUFA induce FADS3 alternative transcripts via PPAR\\u03b3 placed FADS3 in a regulatory regime opposite to that of FADS1/FADS2.\",\n      \"evidence\": \"Dietary LCPUFA intervention in baboon neonate liver and HepG2 cells with PPAR\\u03b3 antagonist GW9662\",\n      \"pmids\": [\"22398025\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct PPAR\\u03b3 binding to FADS3 regulatory elements not demonstrated\", \"Functional consequence of transcript induction not measured\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"FADS3 had no assigned enzymatic activity; in vitro desaturation of trans-vaccenate to a trans11,cis13-CLA isomer provided the first functional characterization of a mammalian methyl-end fatty acid desaturase.\",\n      \"evidence\": \"In vitro desaturase activity assay with rat FADS3, product structural characterization, and siRNA knockdown in rat hepatocytes\",\n      \"pmids\": [\"24070791\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological relevance in vivo not established\", \"Electron donor and cofactor requirements not defined here\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The subcellular behavior of FADS3 was unknown; finding that the 51 kDa isoform is cytosolic, secreted on fibronectin fibers via exosome-like vesicles, and present in serum revealed an unexpected extracellular distribution distinct from other desaturases.\",\n      \"evidence\": \"Subcellular fractionation, confocal imaging, exosome characterization, and serum immunodetection in rat hepatocytes\",\n      \"pmids\": [\"23966218\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role of secreted FADS3 not established\", \"Mechanism of secretion not defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Whether FADS3 contributes to PUFA homeostasis in vivo was unclear; knockout mice revealed altered DHA/DPA balance supporting brain DHA accretion, while showing the in vitro \\u039413-CLA activity does not operate in liver or heart.\",\n      \"evidence\": \"Fads3 knockout mouse fatty acid profiling by gas chromatography and qRT-PCR of related genes\",\n      \"pmids\": [\"28838557\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which Fads3 loss alters DHA synthesis unresolved\", \"Tissue context where \\u039413-desaturation operates not identified\", \"Negative in vivo result conflicts with in vitro activity\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"The principal physiological substrate of FADS3 was redefined; identification as a \\u039414Z long-chain base and ceramide desaturase producing sphingadiene sphingolipids established a sphingolipid rather than fatty-acid-centric role, and linked FADS3 to detoxification of 1-deoxysphinganine.\",\n      \"evidence\": \"Metabolic labeling, overexpression/knockdown, KO mouse LCB profiling, GWAS association, and biochemical ceramide desaturase identification with microdomain fractionation\",\n      \"pmids\": [\"31862735\", \"31916624\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of substrate selectivity not resolved\", \"Cofactor requirements not yet defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The enzymatic mechanism was incompletely defined; establishing that ceramide (not free sphingosine) is the obligate substrate, with chain-length specificity for the sphingosine moiety and NADH/NADPH-cytochrome b5 cofactor dependence, completed the biochemical model and traced flux toward sphingomyelin.\",\n      \"evidence\": \"Cell-based assay with ceramide synthase inhibitor, in vitro enzymatic assay with defined substrates, and cofactor requirement analysis\",\n      \"pmids\": [\"37209771\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of the catalytic site\", \"Regulation of substrate access not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A role in disease was unknown; in ccRCC FADS3 was shown to drive proliferation and EMT through lipid-droplet-derived acetyl-CoA promoting Smad2 acetylation and autocrine TGF-\\u03b2/Smad2/3 signaling.\",\n      \"evidence\": \"Co-immunoprecipitation, mass spectrometry, proliferation/EMT assays, and Smad2/3 phosphorylation/acetylation biochemistry\",\n      \"pmids\": [\"41314810\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Link between desaturase activity and acetyl-CoA generation not mechanistically resolved\", \"Single study without independent replication\", \"Direct FADS3 interaction partners not validated reciprocally\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how FADS3 sphingolipid desaturase activity, the tissue-restricted fatty acid \\u039413-desaturase activity, and the secreted/oncogenic functions are mechanistically connected within a single protein, and whether distinct isoforms underlie these distinct activities.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model linking activities\", \"Isoform-specific function not mapped to catalytic roles\", \"Physiological substrate hierarchy across tissues unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016491\", \"supporting_discovery_ids\": [0, 2, 3, 4]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [2, 3, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 2, 3, 4, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CYB5A\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}