{"gene":"FES","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":1994,"finding":"The SH2 domain of fps/fes selects phosphopeptides with the optimal motif phospho-Tyr-hydrophilic-hydrophilic-hydrophobic (Group I SH2 specificity), established using a degenerate phosphopeptide library screen.","method":"Degenerate phosphopeptide library binding assay","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical assay with defined motif output, single study, no mutagenesis validation of the fps/fes SH2 specifically","pmids":["7511210"],"is_preprint":false},{"year":1983,"finding":"The v-fps transforming gene (without gag sequences) encodes a ~91 kDa protein with associated protein kinase activity and is sufficient for cell transformation and tumor induction, demonstrating that the gag portion of gag-fps fusion is not required for transformation.","method":"Transfection of cloned viral DNA, immunoprecipitation, in vitro kinase assay, tumor induction in chicks","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct functional demonstration with kinase assay and transformation readout, multiple orthogonal methods in one study","pmids":["6605429"],"is_preprint":false},{"year":1983,"finding":"The avian v-fps and mammalian v-fes transforming genes correspond to a single conserved cellular locus (c-fps/fes), with translational products exhibiting protein-tyrosine kinase activity.","method":"Molecular hybridization, sequence comparison, biochemical characterization of kinase activity","journal":"Virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cross-species molecular analysis with functional kinase characterization, independently confirmed by multiple viral isolates","pmids":["6301150"],"is_preprint":false},{"year":1985,"finding":"The human c-fps/fes product p92c-fes is a 92 kDa protein with tyrosine-specific kinase activity in vitro, capable of autophosphorylation and phosphorylation of exogenous substrate enolase; expression is largely confined to myeloid hematopoietic cells.","method":"Immunoprecipitation with anti-fps antiserum, in vitro kinase assay with enolase substrate, cell fractionation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct in vitro kinase assay with substrate phosphorylation, replicated across multiple labs and papers","pmids":["2426571"],"is_preprint":false},{"year":1985,"finding":"NCP92 (p92c-fes) expression is restricted to cells of the monocyte/macrophage and granulocyte lineages in bone marrow and is not found in B-lymphocytic, T-lymphocytic, or erythroid cells; NCP92 has associated tyrosine kinase activity.","method":"Anti-peptide antibody immunoprecipitation, kinase activity assay, analysis of hematopoietic tumors by lineage","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal antibody-based detection with kinase assay, replicated in multiple cell types and independently confirmed","pmids":["2986115"],"is_preprint":false},{"year":1987,"finding":"The minimal catalytic domain of v-fps (P130gag-fps) begins at the predicted N-terminus of the ATP-binding site (residue 922); polypeptides containing ≥263 C-terminal residues are enzymatically active, autophosphorylate at physiological sites, and phosphorylate exogenous substrates (enolase, poly(glu,tyr)).","method":"Expression of trpE-v-fps hybrid proteins in E. coli, in vitro kinase assay, deletion mapping","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with systematic deletion mutagenesis defining catalytic domain boundaries, single lab but multiple constructs and orthogonal substrates","pmids":["2449646"],"is_preprint":false},{"year":1985,"finding":"The c-fps gene product NCP98 (chicken) and its mammalian counterpart NCP92 show highest expression in macrophages and granulocytic cells; NCP98 kinase activity per cell correlates with peak granulopoiesis in bone marrow, spleen, and bursa.","method":"BSA density gradient fractionation of bone marrow cells, kinase activity measurement, complement-mediated lysis depletion","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct fractionation experiment with functional kinase readout, consistent with independent findings in human cells","pmids":["2987674"],"is_preprint":false},{"year":1985,"finding":"The human c-fps/fes gene has a 13 kb genomic locus with 18 exons encoding a 93,390 Da protein (NCP92), deduced from nucleotide sequence; the gene architecture resembles the chicken c-fps locus.","method":"Nucleotide sequencing, Southern blot analysis, sequence deduction","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — complete gene structure determination, single study but comprehensive sequencing","pmids":["4065096"],"is_preprint":false},{"year":1988,"finding":"Human p92c-fes expressed ectopically in Rat-2 fibroblasts is non-transforming despite ~50-fold overexpression; its kinase activity is restrained in vivo (no increase in cellular phosphotyrosine), even though the isolated protein is catalytically active in vitro. This in vivo restraint is lifted for v-fps/fes oncoproteins.","method":"Stable transfection, soft agar assay, immunoprecipitation/kinase assay, phosphotyrosine immunoblot, E. coli expression of kinase fragment","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — multiple orthogonal methods (transformation assay, in vivo phosphotyrosine, in vitro kinase), mechanistically informative negative result with positive in vitro control","pmids":["3352601"],"is_preprint":false},{"year":1989,"finding":"FER (the human counterpart of rat flk) encodes a widely expressed 94 kDa protein-tyrosine kinase antigenically and structurally related to fps/fes; FER and fps/fes define a new subfamily of non-receptor PTKs sharing domain structure.","method":"cDNA cloning, sequencing, immunoblot with anti-fps antiserum, evolutionary conservation analysis","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — structural and antigenic characterization establishing subfamily membership, single lab","pmids":["2685575"],"is_preprint":false},{"year":1990,"finding":"A 13 kb genomic fragment of human c-fps/fes is sufficient for integration-independent, myeloid-specific expression in transgenic mice; expression is proportional to transgene copy number and recapitulates the endogenous myeloid expression pattern.","method":"Transgenic mouse generation, RNase protection, tissue distribution analysis","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct in vivo transgenic experiment defining the cis-acting locus, single lab","pmids":["2188092"],"is_preprint":false},{"year":1992,"finding":"v-Fps induces Egr-1 promoter activation as a primary response (without protein synthesis); this responsiveness is mediated by serum response elements (SREs/CArG boxes) in the Egr-1 promoter, linking v-Fps tyrosine kinase activity to SRE-dependent transcription.","method":"Transient transfection with CAT reporter, deletion mutagenesis of Egr-1 promoter, co-transfection with v-Fps expression vector","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — promoter deletion mapping with functional reporter assay, single lab","pmids":["1594452"],"is_preprint":false},{"year":1993,"finding":"GM-CSF and IL-3 induce tyrosine phosphorylation and kinase activation of p92c-fes in TF-1 cells, and GM-CSF induces physical association between p92c-fes and the beta chain of the GM-CSF receptor, placing c-fps/fes downstream of these hematopoietic growth factor receptors.","method":"Immunoprecipitation, in vitro kinase assay, co-immunoprecipitation of p92c-fes with GM-CSF receptor beta chain","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and kinase activation assay, two orthogonal methods showing both physical association and functional activation","pmids":["7682176"],"is_preprint":false},{"year":1993,"finding":"Erythropoietin (EPO) induces tyrosine phosphorylation and enhanced kinase activity of p92c-fes in human erythroleukemia TF-1 cells, implicating c-fps/fes in EPO receptor signaling.","method":"Immunoprecipitation, in vitro kinase assay, anti-phosphotyrosine immunoblot","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, immunoprecipitation and kinase assay, no direct receptor interaction demonstrated","pmids":["7685196"],"is_preprint":false},{"year":1994,"finding":"Activated (myristylated) Fps/Fes transforms Rat-2 fibroblasts and drives widespread hypervascularity progressing to multifocal hemangiomas in transgenic mice; fps/fes transcripts localize to endothelial cells of vascular tumors and normal blood vessels, indicating a direct role in angiogenesis regulation.","method":"Retroviral transformation assay, transgenic mouse model, in situ RNA hybridization, RNase protection","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (transformation, transgenic model, in situ hybridization) in one study, clear functional phenotype","pmids":["7523858"],"is_preprint":false},{"year":1995,"finding":"Spi-1/PU.1 and Spi-B transcription factors bind a site in the c-fes/c-fps promoter and activate c-fes transcription; Spi-1 binds this site in vivo in HL-60 cells, suggesting Spi-1 regulates myeloid-specific c-fes expression.","method":"PCR-mediated random site selection, in vitro binding/transcription assay, transfection in HeLa cells, gel shift with HL-60 nuclear extracts","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding plus in vivo chromatin/gel shift evidence, single lab but multiple orthogonal methods","pmids":["7624145"],"is_preprint":false},{"year":1995,"finding":"FES phosphorylates BCR on tyrosine residues upon co-expression in Sf-9 cells, forming a stable BCR-FES complex; this interaction involves the FES SH2 domain and a novel N-terminal BCR-binding domain (first 347 aa of FES). Tyrosine-phosphorylated BCR then associates with GRB-2/SOS, linking FES to RAS signaling. Deletion of the N-terminal BCR-binding domain from v-fps abolished transforming activity.","method":"Co-expression in Sf-9 insect cells, co-immunoprecipitation, deletion mutagenesis, transformation assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP with domain mapping mutagenesis and functional transformation readout, multiple orthogonal methods","pmids":["7529874"],"is_preprint":false},{"year":1996,"finding":"Endothelial cells from hypervascular fps/fes transgenic mouse yolk sacs show a growth advantage and express high levels of the fps/fes tyrosine kinase, supporting a role in vasculogenesis and angiogenesis.","method":"Cell cloning from transgenic yolk sac, Southern blot genotyping, immunoblot for fps/fes expression, Matrigel tube formation assay","journal":"In vitro cellular & developmental biology. Animal","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — cell biological characterization with functional endothelial assay, single lab","pmids":["8792159"],"is_preprint":false},{"year":1997,"finding":"fps-transformed fibroblasts show approximately 2-fold elevated concentrations of phosphatidate and diacylglycerol compared to controls, resulting from enhanced phospholipid turnover; ceramide concentrations are also elevated ~2.5-fold, linking fps tyrosine kinase activity to bioactive lipid second messenger pathways.","method":"Lipid extraction and quantification, phospholipid turnover assay, phosphatase/kinase activity measurements","journal":"Oncogene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — biochemical measurements in transformed cells, indirect mechanistic link, single lab","pmids":["9129148"],"is_preprint":false},{"year":1998,"finding":"Fps/Fes-induced fibroblast transformation requires Ras, Rac, and Cdc42; ERK activation by v-Fps/Myr-Fes occurs exclusively downstream of Ras, while JNK activation requires both Ras and Rho-family GTPases (Rac and Cdc42), defining the small G protein/MAPK cascades through which Fps/Fes signals.","method":"Dominant-negative small G protein co-expression, soft agar transformation assay, ERK and JNK kinase activity measurements","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with dominant-negatives plus direct kinase assays, multiple pathways dissected, single lab","pmids":["9593727"],"is_preprint":false},{"year":1998,"finding":"v-Fps induces tyrosine phosphorylation and activation of the PDGFbeta receptor within minutes of kinase activation; sustained v-Fps expression causes >100-fold downregulation of PDGF receptor protein. Kinase activity of v-Fps is required for both PDGF receptor phosphorylation and downregulation. A kinase-inactive PDGF receptor cannot mediate transformation even when phosphorylated by v-Fps.","method":"Immunoprecipitation/kinase assay, immunoblot, soft agar colony formation assay, kinase-inactive PDGF receptor mutant co-expression","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods with mutagenesis validation, single lab","pmids":["9620549"],"is_preprint":false},{"year":1999,"finding":"Kinase-inactivating missense mutation in murine fps/fes results in dramatically reduced Stat3 and Stat5A tyrosine phosphorylation in response to GM-CSF (but not IL-3 or IL-6) in bone marrow-derived macrophages, and reduced LPS-induced Erk1/2 activation, demonstrating a non-redundant role for Fps/Fes kinase activity in GM-CSF receptor signaling.","method":"Knock-in mouse model, flow cytometry, signaling analysis by immunoblot, bone marrow colony-forming assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — defined kinase-inactivating knock-in with specific signaling readouts, replicated independently","pmids":["10523632"],"is_preprint":false},{"year":2001,"finding":"Fps/Fes localizes to cytoplasmic vesicles and a perinuclear Golgi region (colocalizing with TGN38), and also colocalizes with Rab proteins involved in both endocytosis (Rab5B, Rab7) and exocytosis (Rab1A, Rab3A); this localization is disrupted by brefeldin A. Fer is diffusely cytoplasmic. This distinct vesicular localization suggests a role for Fps/Fes in vesicular trafficking.","method":"GFP fusion proteins, confocal fluorescence microscopy, colocalization with TGN38 and Rab markers, brefeldin A perturbation","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct live-cell imaging with multiple colocalization markers and pharmacological perturbation, single lab","pmids":["11339827"],"is_preprint":false},{"year":2002,"finding":"Fps/Fes-null mice are more sensitive to LPS-induced endotoxicity; fps/fes kinase is involved in but not required for myelopoiesis; phenotypes are rescued by fps/fes transgene. Fps/Fes-null macrophages show no defects in GM-CSF-, IL-6-, or IL-3-induced Stat3/Stat5A activation or LPS-induced IκB degradation, p38, JNK, ERK, or Akt activation.","method":"Fps/fes-null mouse model, LPS challenge, flow cytometry, signaling analysis by immunoblot, transgene rescue","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — null mouse with transgene rescue, comprehensive signaling panel, multiple orthogonal readouts","pmids":["11909942"],"is_preprint":false},{"year":2002,"finding":"Fes/Fps tyrosine kinase interacts with plexinA1 (PlexA1) and phosphorylates PlexA1 on tyrosine; neuropilin-1 (NP-1) attenuates this interaction in resting conditions but semaphorin3A (Sema3A) enhances Fes-PlexA1 association and Fes-mediated phosphorylation of PlexA1, CRAM, and CRMP2. Fes kinase-negative mutants suppress Sema3A-induced growth cone collapse, placing Fes in the Sema3A signaling pathway.","method":"Co-immunoprecipitation in COS-7 cells, cell morphology assay, dominant-negative kinase mutant, DRG neuron growth cone collapse assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP with dominant-negative mutagenesis and two functional readouts (cell contraction, growth cone collapse), single lab but multiple orthogonal methods","pmids":["12093729"],"is_preprint":false},{"year":2003,"finding":"Fps/Fes and Fer are expressed in platelets and are activated following collagen/CRP stimulation (GPVI pathway); Fer is also activated by thrombin/PAR4. Fps/Fes-null platelets show increased collagen-induced aggregation and elevated P-selectin surface expression; Fer-deficient platelets disaggregate more rapidly in response to ADP, demonstrating roles for these kinases in platelet aggregation regulation.","method":"Immunoprecipitation/kinase assay from platelet lysates, platelet aggregometry, P-selectin flow cytometry, targeted knockout mouse models","journal":"Journal of thrombosis and haemostasis : JTH","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple functional assays with knockout mouse models, single lab","pmids":["12871378"],"is_preprint":false},{"year":2003,"finding":"Fes tyrosine kinase associates with microtubules and promotes microtubule bundling in a kinase-dependent manner; the FCH (Fes/CIP4 homology) domain of Fes colocalizes with gamma-tubulin at microtubule nucleation sites. FCH-deleted Fes blocks centrosome formation, and Fes-deficient mouse embryonic fibroblasts display aberrant microtubule nucleation and centrosome structure.","method":"Confocal microscopy, co-localization with gamma-tubulin, microtubule regeneration assay, FCH deletion mutants, Fes-deficient MEFs","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct imaging with domain mutagenesis and knockout MEF validation, single lab","pmids":["14551201"],"is_preprint":false},{"year":2003,"finding":"Mice lacking both Fps and Fer kinase activities are viable but show reduced fertility, elevated circulating neutrophils/erythrocytes/platelets, reduced bone marrow cellularity, and elevated CD11b(hi)Ly-6G(lo) myeloid cells, demonstrating functional redundancy between Fps and Fer in regulating hematopoiesis.","method":"Compound knock-in mouse model, flow cytometry, peripheral blood counts, bone marrow colony-forming assays","journal":"Experimental hematology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — double kinase-inactivating knock-in model with comprehensive hematopoietic analysis, single lab","pmids":["12901971"],"is_preprint":false},{"year":2005,"finding":"Three of four somatic fps/fes kinase domain mutations found in colorectal cancers result in kinase inactivation, not activation; a fourth compromises in vivo activity. Tumor onset is accelerated in mice with fps/fes null or kinase-inactivating mutations in a breast cancer model, and restored by fps/fes transgene, suggesting a tumor suppressor role for Fps/Fes in epithelial cells.","method":"Biochemical kinase assays of mutant proteins, structural modeling, transgenic/knock-in mouse tumor model, tumor onset kinetics","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro kinase assay of cancer-derived mutants combined with in vivo mouse tumor model and transgene rescue, multiple orthogonal approaches","pmids":["15867340"],"is_preprint":false},{"year":2006,"finding":"Fps/Fes-null macrophages display prolonged LPS-induced IκBα degradation, increased NF-κB p65 phosphorylation, increased TNF-α production, and defective TLR4 internalization compared to wild-type macrophages. This provides a mechanistic basis for enhanced endotoxin sensitivity of Fps/Fes-null mice: Fps/Fes modulates innate immune responses partly by regulating TLR4 internalization.","method":"Fps/fes-null macrophage culture, ELISA for TNF-α, immunoblot for IκBα and phospho-p65, TLR4 internalization assay","journal":"Journal of leukocyte biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — null macrophages with multiple orthogonal signaling readouts and defined phenotypic mechanism, single lab","pmids":["16959897"],"is_preprint":false},{"year":2006,"finding":"FcεRI aggregation in mast cells leads to increased Fer/Fps kinase activities in a Lyn-dependent manner (independent of Syk, Fyn, and Gab2). Activated Fer/Fps phosphorylate PECAM-1 ITIMs and Tyr700 in vitro and in transfected cells. Mast cells devoid of Fer/Fps kinase activities show reduced PECAM-1 phosphorylation and exaggerated degranulation at low antigen doses.","method":"Kinase activity assay, in vitro phosphorylation of PECAM-1, transfected cell phosphorylation, mast cells from kinase-deficient mice, degranulation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — direct in vitro substrate phosphorylation combined with genetic mouse models and defined cellular phenotype, multiple orthogonal methods","pmids":["16731527"],"is_preprint":false},{"year":2007,"finding":"FES is phosphorylated on tyrosine residues in cells harboring KIT(D816V) in a KIT-dependent manner; RNAi-mediated reduction of FES expression decreases cell proliferation in human and murine cells with KIT(D816V) or KIT(D814Y), and the growth defect is rescued by GM-CSF. FES knockdown alters signaling downstream of KIT(D816V), identifying FES as an essential effector of oncogenic KIT.","method":"RNAi knockdown, proliferation assay, phosphotyrosine immunoblot, GM-CSF rescue, signaling analysis","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 / Moderate — RNAi knockdown with functional rescue, specific signaling analysis, comparison with FER knockdown, single lab but multiple orthogonal methods","pmids":["17595334"],"is_preprint":false},{"year":2010,"finding":"Both FES and FER are activated in AML blasts and cell lines in a FLT3-dependent manner; RNAi knockdown of FES or FER inhibits proliferation downstream of FLT3-ITD, with FER required for cell cycle transitions and FES necessary for cell survival, demonstrating non-redundant functions of FES and FER downstream of oncogenic FLT3.","method":"RNAi knockdown, proliferation/cell cycle/survival assays in AML cell lines, activation status by immunoprecipitation/kinase assay","journal":"Leukemia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNAi with multiple functional readouts distinguishing FES vs FER roles, single lab","pmids":["20111072"],"is_preprint":false},{"year":2022,"finding":"CRISPR-engineered monocytic cell lines with 15q26.1 CAD risk genotype have reduced FES expression. FES knockdown promotes migration of monocytes and vascular smooth muscle cells and alters phosphorylation of migration-regulating proteins (phosphoproteomics). Fes knockout in ApoE-deficient mice increases atherosclerotic plaque size and monocyte/macrophage and smooth muscle cell content, identifying FES as a protective factor against atherosclerosis.","method":"CRISPR genome editing, siRNA knockdown, phosphoproteomics, migration assays, scRNA-seq, Fes knockout in ApoE-deficient mouse atherosclerosis model","journal":"Circulation research","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods including CRISPR editing, phosphoproteomics, and in vivo mouse model with defined phenotype","pmids":["36321446"],"is_preprint":false}],"current_model":"FES (c-Fps/Fes) is a cytoplasmic non-receptor protein-tyrosine kinase that is activated downstream of hematopoietic growth factor receptors (GM-CSF, IL-3, EPO) and immune receptors (FcεRI, KIT, FLT3), where it phosphorylates substrates including BCR, PECAM-1, PlexA1, CRMP2, and the PDGFβ receptor; its kinase activity is restrained in normal cells through regulatory interactions but activated in oncogenic contexts; it signals through Ras/Rac/Cdc42 to ERK and JNK, regulates TLR4 internalization to limit innate immune responses, localizes to Golgi/vesicular compartments suggesting a role in vesicular trafficking, and promotes microtubule nucleation and bundling through its FCH domain, with overall roles in myeloid differentiation, angiogenesis, platelet aggregation, semaphorin signaling, and atherosclerosis suppression."},"narrative":{"mechanistic_narrative":"FES (c-Fps/Fes) is a cytoplasmic non-receptor protein-tyrosine kinase expressed predominantly in myeloid hematopoietic cells (monocyte/macrophage and granulocyte lineages) that acts as a signaling effector downstream of hematopoietic growth factor and immune receptors [PMID:2426571, PMID:2986115]. The mature protein autophosphorylates and phosphorylates exogenous tyrosine substrates in vitro, and its catalytic activity resides in a C-terminal kinase domain while its SH2 domain selects Group I phosphopeptide motifs (phospho-Tyr-hydrophilic-hydrophilic-hydrophobic) [PMID:7511210, PMID:2449646]. Although intrinsically active in vitro, FES kinase activity is restrained in normal cells, and this restraint is relieved in oncogenic v-fps/fes forms that drive cellular transformation [PMID:6605429, PMID:3352601]. FES is activated by GM-CSF, IL-3, and EPO and physically associates with the GM-CSF receptor beta chain, with kinase-inactivating knock-in mice revealing a non-redundant requirement for FES in GM-CSF-induced Stat3/Stat5A phosphorylation [PMID:7682176, PMID:10523632]. Downstream, FES phosphorylates BCR to nucleate a GRB2/SOS complex and signals through Ras to ERK and through Ras plus Rac/Cdc42 to JNK [PMID:7529874, PMID:9593727]. FES also phosphorylates the PDGFbeta receptor, plexinA1/CRMP2 in semaphorin3A-induced growth cone collapse, and PECAM-1 ITIMs downstream of FcepsilonRI to restrain mast cell degranulation [PMID:9620549, PMID:12093729, PMID:16731527]. In innate immunity it limits TLR4 signaling by promoting receptor internalization, accounting for endotoxin hypersensitivity of FES-null mice [PMID:11909942, PMID:16959897]. Beyond signaling, FES localizes to Golgi and Rab-marked vesicular compartments and, via its FCH domain, associates with microtubules and gamma-tubulin to promote microtubule bundling and centrosomal nucleation [PMID:11339827, PMID:14551201]. FES is an essential effector of oncogenic KIT and FLT3-ITD in leukemic cells, yet functions as a tumor suppressor in epithelial cancers and protects against atherosclerosis by restraining monocyte and smooth muscle cell migration [PMID:15867340, PMID:17595334, PMID:20111072, PMID:36321446].","teleology":[{"year":1983,"claim":"Established that the transforming activity of the fps/fes oncogene resides in a tyrosine kinase encoded by a single conserved cellular locus, defining the gene's core biochemical identity.","evidence":"Cloned viral DNA transfection, immunoprecipitation/in vitro kinase assay, tumor induction, and cross-species molecular hybridization","pmids":["6605429","6301150"],"confidence":"Medium","gaps":["Did not define the cellular substrates or physiological regulators of the normal c-fps/fes product","Transformation readouts used viral oncogene, not the proto-oncogene"]},{"year":1985,"claim":"Defined the human proto-oncogene product p92c-fes as a myeloid-restricted tyrosine kinase, linking the kinase to a specific hematopoietic lineage.","evidence":"Anti-peptide antibody immunoprecipitation, in vitro kinase/enolase phosphorylation, lineage analysis of hematopoietic cells and gene structure determination","pmids":["2426571","2986115","2987674","4065096"],"confidence":"High","gaps":["Did not identify activating receptors or physiological substrates","Mechanism of lineage-restricted expression unresolved at this stage"]},{"year":1987,"claim":"Mapped the minimal catalytic domain, showing the C-terminal kinase region alone is sufficient for autophosphorylation and substrate phosphorylation.","evidence":"E. coli expression of trpE-v-fps deletion constructs with in vitro kinase assays","pmids":["2449646"],"confidence":"High","gaps":["Used viral v-fps, not the regulated cellular protein","Did not address how N-terminal/SH2 regions regulate activity in cells"]},{"year":1988,"claim":"Revealed that the normal kinase is intrinsically active yet held in check in vivo, distinguishing the proto-oncogene from its transforming viral counterpart.","evidence":"Stable overexpression in Rat-2 fibroblasts with soft agar, in vivo phosphotyrosine immunoblot, and in vitro kinase controls","pmids":["3352601"],"confidence":"High","gaps":["Molecular basis of the in vivo restraint not defined","Did not identify the cellular context where restraint is physiologically relieved"]},{"year":1993,"claim":"Placed c-fps/fes downstream of hematopoietic cytokine receptors by demonstrating receptor-induced activation and physical receptor association.","evidence":"Immunoprecipitation/kinase assay and co-IP with GM-CSF receptor beta chain in TF-1 cells; EPO-induced activation","pmids":["7682176","7685196"],"confidence":"High","gaps":["EPO receptor interaction not demonstrated directly","Downstream substrates of receptor-activated FES not yet defined"]},{"year":1995,"claim":"Identified BCR as a FES substrate that couples the kinase to Ras signaling and showed the N-terminal BCR-binding domain is required for transformation.","evidence":"Co-expression in Sf-9 cells, co-IP, SH2/domain deletion mutagenesis, and transformation assay","pmids":["7529874"],"confidence":"High","gaps":["Interaction mapped in heterologous insect cells","Physiological role of BCR-FES complex in myeloid cells not established"]},{"year":1998,"claim":"Dissected the GTPase/MAPK architecture downstream of FES, separating Ras-dependent ERK activation from Ras/Rac/Cdc42-dependent JNK activation.","evidence":"Dominant-negative small G protein co-expression with soft agar and ERK/JNK kinase assays; PDGFbeta receptor phosphorylation/downregulation experiments","pmids":["9593727","9620549"],"confidence":"High","gaps":["Used activated Fps/Fes transformation context, not normal signaling","Direct linkage between FES substrates and GTPase activation incompletely defined"]},{"year":1999,"claim":"Demonstrated a non-redundant, kinase-dependent requirement for FES in GM-CSF receptor signaling in vivo via a knock-in mouse.","evidence":"Kinase-inactivating knock-in mouse, immunoblot of Stat3/Stat5A and Erk1/2 in bone marrow-derived macrophages","pmids":["10523632"],"confidence":"High","gaps":["Specificity to GM-CSF over IL-3/IL-6 mechanistically unexplained","Direct STAT phosphorylation by FES not shown"]},{"year":2001,"claim":"Localized FES to Golgi and Rab-marked vesicular compartments, implicating it in vesicular trafficking and distinguishing it from diffusely cytoplasmic Fer.","evidence":"GFP-fusion confocal imaging, colocalization with TGN38 and Rab markers, brefeldin A perturbation","pmids":["11339827"],"confidence":"Medium","gaps":["Functional consequence of vesicular localization for trafficking not tested","Single-lab imaging without orthogonal biochemical fractionation"]},{"year":2002,"claim":"Extended FES function beyond hematopoiesis into innate immunity and axon guidance, defining roles in endotoxin response and semaphorin signaling.","evidence":"Fps/fes-null mice with LPS challenge and signaling panels; co-IP and growth cone collapse assays for the PlexA1/Sema3A pathway","pmids":["11909942","12093729"],"confidence":"High","gaps":["Mechanism connecting FES to endotoxin sensitivity not yet defined in 2002","PlexA1 interaction characterized in COS-7 overexpression"]},{"year":2003,"claim":"Uncovered cytoskeletal and platelet functions and established functional redundancy with Fer in hematopoiesis.","evidence":"Microtubule bundling/gamma-tubulin colocalization with FCH deletion in MEFs; platelet aggregometry and P-selectin assays; compound Fps/Fer kinase-inactivating knock-in mice","pmids":["14551201","12871378","12901971"],"confidence":"Medium","gaps":["Microtubule and platelet substrates of FES not identified","Mechanism of FCH-mediated microtubule nucleation incompletely defined"]},{"year":2005,"claim":"Revealed a context-dependent tumor suppressor role in epithelial cancers, with cancer-associated mutations inactivating rather than activating the kinase.","evidence":"Biochemical kinase assays of colorectal cancer-derived mutants, structural modeling, breast cancer mouse model with null/knock-in alleles and transgene rescue","pmids":["15867340"],"confidence":"High","gaps":["Epithelial substrates mediating tumor suppression not identified","Reconciliation of suppressor versus oncogenic roles mechanistically open"]},{"year":2006,"claim":"Provided mechanistic basis for FES control of innate immunity and immune-receptor signaling via TLR4 internalization and PECAM-1 phosphorylation.","evidence":"Fps/fes-null macrophages with TLR4 internalization assays, NF-kB readouts; FcepsilonRI-activated mast cells with in vitro PECAM-1 phosphorylation and degranulation assays","pmids":["16959897","16731527"],"confidence":"High","gaps":["How FES promotes TLR4 internalization at the molecular level unresolved","Lyn-to-FES activation step in mast cells not fully mapped"]},{"year":2010,"claim":"Established FES (with FER) as a non-redundant effector of oncogenic receptor tyrosine kinases in leukemia.","evidence":"RNAi knockdown with proliferation/survival/cell-cycle assays in KIT(D816V) and FLT3-ITD cells, with kinase activation status and GM-CSF rescue","pmids":["17595334","20111072"],"confidence":"High","gaps":["Direct FES substrates downstream of KIT/FLT3 not defined","Whether FES is directly phosphorylated by these receptors versus indirectly activated unclear"]},{"year":2022,"claim":"Linked a human CAD risk locus to reduced FES expression and a protective role against atherosclerosis through restraint of cell migration.","evidence":"CRISPR genotype editing, siRNA, phosphoproteomics, migration assays, scRNA-seq, and Fes knockout in ApoE-deficient atherosclerosis model","pmids":["36321446"],"confidence":"High","gaps":["Specific FES substrates governing migration not pinpointed","Cell-type-specific contributions of monocyte versus smooth muscle FES not separated"]},{"year":null,"claim":"The molecular basis for the in vivo restraint of FES kinase activity and how the same kinase functions as both an oncogenic effector and a tumor/atherosclerosis suppressor across cell types remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying structural mechanism for context-dependent activation/restraint","Physiological direct substrates in epithelial and vascular settings not catalogued","Vesicular and microtubule functions not connected to a defined signaling output"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[3,5,16,20,24,30]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[3,5]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[26]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[22]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[22]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[26]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[26]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[12,19,24]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[23,29,30]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[28,31,32,33]},{"term_id":"R-HSA-109582","term_label":"Hemostasis","supporting_discovery_ids":[25]}],"complexes":[],"partners":["BCR","PLEXINA1","PECAM1","PDGFRB","CSF2RB","KIT","FLT3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P07332","full_name":"Tyrosine-protein kinase Fes/Fps","aliases":["Feline sarcoma/Fujinami avian sarcoma oncogene homolog","Proto-oncogene c-Fes","Proto-oncogene c-Fps","p93c-fes"],"length_aa":822,"mass_kda":93.5,"function":"Tyrosine-protein kinase that acts downstream of cell surface receptors and plays a role in the regulation of the actin cytoskeleton, microtubule assembly, cell attachment and cell spreading. 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Patients With Breast Cancer.","date":"2022","source":"Seminars in nuclear medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35379454","citation_count":41,"is_preprint":false},{"pmid":"21936771","id":"PMC_21936771","title":"Mutation in the Fe-S scaffold protein Isu bypasses frataxin deletion.","date":"2012","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/21936771","citation_count":41,"is_preprint":false},{"pmid":"27517714","id":"PMC_27517714","title":"The DUF59 Containing Protein SufT Is Involved in the Maturation of Iron-Sulfur (FeS) Proteins during Conditions of High FeS Cofactor Demand in Staphylococcus aureus.","date":"2016","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/27517714","citation_count":41,"is_preprint":false},{"pmid":"17595334","id":"PMC_17595334","title":"The tyrosine kinase FES is an essential effector of KITD816V proliferation signal.","date":"2007","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/17595334","citation_count":40,"is_preprint":false},{"pmid":"36321446","id":"PMC_36321446","title":"The FES Gene at the 15q26 Coronary-Artery-Disease Locus Inhibits Atherosclerosis.","date":"2022","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/36321446","citation_count":39,"is_preprint":false},{"pmid":"10523632","id":"PMC_10523632","title":"Targeted disruption of the murine fps/fes proto-oncogene reveals that Fps/Fes kinase activity is dispensable for hematopoiesis.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10523632","citation_count":39,"is_preprint":false},{"pmid":"36893757","id":"PMC_36893757","title":"Oxygen toxicity causes cyclic damage by destabilizing specific Fe-S cluster-containing protein complexes.","date":"2023","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/36893757","citation_count":38,"is_preprint":false},{"pmid":"27262547","id":"PMC_27262547","title":"Reductive transformation of hexabromocyclododecane (HBCD) by FeS.","date":"2016","source":"Water research","url":"https://pubmed.ncbi.nlm.nih.gov/27262547","citation_count":38,"is_preprint":false},{"pmid":"2449646","id":"PMC_2449646","title":"Catalytic and non-catalytic domains of the Fujinami sarcoma virus P130gag-fps protein-tyrosine kinase distinguished by the expression of v-fps polypeptides in Escherichia coli.","date":"1987","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/2449646","citation_count":38,"is_preprint":false},{"pmid":"11339827","id":"PMC_11339827","title":"Subcellular localization analysis of the closely related Fps/Fes and Fer protein-tyrosine kinases suggests a distinct role for Fps/Fes in vesicular trafficking.","date":"2001","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/11339827","citation_count":36,"is_preprint":false},{"pmid":"3352601","id":"PMC_3352601","title":"The human c-fps/fes gene product expressed ectopically in rat fibroblasts is nontransforming and has restrained protein-tyrosine kinase activity.","date":"1988","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/3352601","citation_count":36,"is_preprint":false},{"pmid":"29626095","id":"PMC_29626095","title":"The ErpA/NfuA complex builds an oxidation-resistant Fe-S cluster delivery pathway.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29626095","citation_count":35,"is_preprint":false},{"pmid":"3023866","id":"PMC_3023866","title":"Antipeptide antiserum identifies a widely distributed cellular tyrosine kinase related to but distinct from the c-fps/fes-encoded protein.","date":"1986","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/3023866","citation_count":35,"is_preprint":false},{"pmid":"9593727","id":"PMC_9593727","title":"Fibroblast transformation by Fps/Fes tyrosine kinases requires Ras, Rac, and Cdc42 and induces extracellular signal-regulated and c-Jun N-terminal kinase activation.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9593727","citation_count":35,"is_preprint":false},{"pmid":"22201778","id":"PMC_22201778","title":"FES/FER kinase signaling in hematopoietic cells and leukemias.","date":"2012","source":"Frontiers in bioscience (Landmark edition)","url":"https://pubmed.ncbi.nlm.nih.gov/22201778","citation_count":34,"is_preprint":false},{"pmid":"20109183","id":"PMC_20109183","title":"Polysaccharide from fuzi (FPS) prevents hypercholesterolemia in rats.","date":"2010","source":"Lipids in health and disease","url":"https://pubmed.ncbi.nlm.nih.gov/20109183","citation_count":34,"is_preprint":false},{"pmid":"16731527","id":"PMC_16731527","title":"Fer and Fps/Fes participate in a Lyn-dependent pathway from FcepsilonRI to platelet-endothelial cell adhesion molecule 1 to limit mast cell activation.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16731527","citation_count":34,"is_preprint":false},{"pmid":"14551201","id":"PMC_14551201","title":"Role for Fes/Fps tyrosine kinase in microtubule nucleation through is Fes/CIP4 homology domain.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/14551201","citation_count":33,"is_preprint":false},{"pmid":"32632277","id":"PMC_32632277","title":"Structural insights into Fe-S protein biogenesis by the CIA targeting complex.","date":"2020","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/32632277","citation_count":33,"is_preprint":false},{"pmid":"16959897","id":"PMC_16959897","title":"The Fps/Fes kinase regulates the inflammatory response to endotoxin through down-regulation of TLR4, NF-kappaB activation, and TNF-alpha secretion in macrophages.","date":"2006","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/16959897","citation_count":32,"is_preprint":false},{"pmid":"17596513","id":"PMC_17596513","title":"Geranylgeranyl diphosphate synthase in fission yeast is a heteromer of farnesyl diphosphate synthase (FPS), Fps1, and an FPS-like protein, Spo9, essential for sporulation.","date":"2007","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/17596513","citation_count":31,"is_preprint":false},{"pmid":"10788513","id":"PMC_10788513","title":"Identification of the [Fe-S] cluster-binding residues of Escherichia coli biotin synthase.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10788513","citation_count":30,"is_preprint":false},{"pmid":"3553615","id":"PMC_3553615","title":"Structure of the feline c-fes/fps proto-oncogene: genesis of a retroviral oncogene.","date":"1987","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/3553615","citation_count":30,"is_preprint":false},{"pmid":"29569085","id":"PMC_29569085","title":"The NMR contribution to protein-protein networking in Fe-S protein maturation.","date":"2018","source":"Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29569085","citation_count":29,"is_preprint":false},{"pmid":"35247854","id":"PMC_35247854","title":"Fe-S clusters masquerading as zinc finger proteins.","date":"2022","source":"Journal of inorganic biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35247854","citation_count":29,"is_preprint":false},{"pmid":"27714045","id":"PMC_27714045","title":"Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20.","date":"2016","source":"Metallomics : integrated biometal science","url":"https://pubmed.ncbi.nlm.nih.gov/27714045","citation_count":28,"is_preprint":false},{"pmid":"1594452","id":"PMC_1594452","title":"v-Fps-responsiveness in the Egr-1 promoter is mediated by serum response elements.","date":"1992","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/1594452","citation_count":28,"is_preprint":false},{"pmid":"29273621","id":"PMC_29273621","title":"RecQ and Fe-S helicases have unique roles in DNA metabolism dictated by their unwinding directionality, substrate specificity, and protein interactions.","date":"2017","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/29273621","citation_count":27,"is_preprint":false},{"pmid":"34440194","id":"PMC_34440194","title":"A Review of Multiple Mitochondrial Dysfunction Syndromes, Syndromes Associated with Defective Fe-S Protein Maturation.","date":"2021","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/34440194","citation_count":27,"is_preprint":false},{"pmid":"12901971","id":"PMC_12901971","title":"Fps/Fes and Fer protein-tyrosinekinases play redundant roles in regulating hematopoiesis.","date":"2003","source":"Experimental hematology","url":"https://pubmed.ncbi.nlm.nih.gov/12901971","citation_count":26,"is_preprint":false},{"pmid":"25196712","id":"PMC_25196712","title":"Fe/S protein biogenesis in trypanosomes - A review.","date":"2014","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/25196712","citation_count":26,"is_preprint":false},{"pmid":"20111072","id":"PMC_20111072","title":"FES kinases are required for oncogenic FLT3 signaling.","date":"2010","source":"Leukemia","url":"https://pubmed.ncbi.nlm.nih.gov/20111072","citation_count":26,"is_preprint":false},{"pmid":"21288761","id":"PMC_21288761","title":"Iron chaperones for mitochondrial Fe-S cluster biosynthesis and ferritin iron storage.","date":"2011","source":"Current opinion in chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/21288761","citation_count":26,"is_preprint":false},{"pmid":"32502492","id":"PMC_32502492","title":"Inhibition of RAGE by FPS-ZM1 alleviates renal injury in spontaneously hypertensive rats.","date":"2020","source":"European journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/32502492","citation_count":26,"is_preprint":false},{"pmid":"1373879","id":"PMC_1373879","title":"Expression of truncated transcripts of the proto-oncogene c-fps/fes in human lymphoma and lymphoid leukemia cell lines.","date":"1992","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/1373879","citation_count":26,"is_preprint":false},{"pmid":"34829609","id":"PMC_34829609","title":"Sulfur Administration in Fe-S Cluster Homeostasis.","date":"2021","source":"Antioxidants (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/34829609","citation_count":25,"is_preprint":false},{"pmid":"15867340","id":"PMC_15867340","title":"An identity crisis for fps/fes: oncogene or tumor suppressor?","date":"2005","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/15867340","citation_count":24,"is_preprint":false},{"pmid":"12871378","id":"PMC_12871378","title":"Fps/Fes and Fer non-receptor protein-tyrosine kinases regulate collagen- and ADP-induced platelet aggregation.","date":"2003","source":"Journal of thrombosis and haemostasis : JTH","url":"https://pubmed.ncbi.nlm.nih.gov/12871378","citation_count":24,"is_preprint":false},{"pmid":"30184127","id":"PMC_30184127","title":"Fe-S Cluster Assembly in Oxymonads and Related Protists.","date":"2018","source":"Molecular biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/30184127","citation_count":24,"is_preprint":false},{"pmid":"29773647","id":"PMC_29773647","title":"Altered sterol metabolism in budding yeast affects mitochondrial iron-sulfur (Fe-S) cluster synthesis.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29773647","citation_count":24,"is_preprint":false},{"pmid":"9620549","id":"PMC_9620549","title":"v-fps causes transformation by inducing tyrosine phosphorylation and activation of the PDGFbeta receptor.","date":"1998","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/9620549","citation_count":23,"is_preprint":false},{"pmid":"37488138","id":"PMC_37488138","title":"The Fe-S cluster assembly protein IscU2 increases α-ketoglutarate catabolism and DNA 5mC to promote tumor growth.","date":"2023","source":"Cell discovery","url":"https://pubmed.ncbi.nlm.nih.gov/37488138","citation_count":21,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":44068,"output_tokens":8368,"usd":0.128862,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":17654,"output_tokens":5010,"usd":0.10676,"stage2_stop_reason":"end_turn"},"total_usd":0.235622,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"Looking through the corpus, I need to identify papers about the canonical FES gene (FES proto-oncogene, tyrosine kinase; also known as FPS). I'll filter out:\n- Fe-S cluster biology papers (completely different topic)\n- FES as fluoroestradiol PET tracer\n- FPS as polysaccharide from fuzi\n- FPS-ZM1 as RAGE inhibitor\n- Fission yeast FPS1 (farnesyl diphosphate synthase)\n- Papers about Fe-S proteins in bacteria/plants/other organisms unrelated to the tyrosine kinase\n\nPapers clearly about the FES/FPS tyrosine kinase: [1], [7], [9], [13], [18], [22], [24], [25], [29], [34], [37], [38], [40], [44], [47], [52], [53], [54], [57], [62], [63], [64], [67], [68], [69], [72], [73], [75], [76], [78], [81], [85], [88], [90], [93], [95], [96], [99]\n\nNow I'll extract mechanistic discoveries from these papers:\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1994,\n      \"finding\": \"The SH2 domain of fps/fes selects phosphopeptides with the optimal motif phospho-Tyr-hydrophilic-hydrophilic-hydrophobic (Group I SH2 specificity), established using a degenerate phosphopeptide library screen.\",\n      \"method\": \"Degenerate phosphopeptide library binding assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical assay with defined motif output, single study, no mutagenesis validation of the fps/fes SH2 specifically\",\n      \"pmids\": [\"7511210\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1983,\n      \"finding\": \"The v-fps transforming gene (without gag sequences) encodes a ~91 kDa protein with associated protein kinase activity and is sufficient for cell transformation and tumor induction, demonstrating that the gag portion of gag-fps fusion is not required for transformation.\",\n      \"method\": \"Transfection of cloned viral DNA, immunoprecipitation, in vitro kinase assay, tumor induction in chicks\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct functional demonstration with kinase assay and transformation readout, multiple orthogonal methods in one study\",\n      \"pmids\": [\"6605429\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1983,\n      \"finding\": \"The avian v-fps and mammalian v-fes transforming genes correspond to a single conserved cellular locus (c-fps/fes), with translational products exhibiting protein-tyrosine kinase activity.\",\n      \"method\": \"Molecular hybridization, sequence comparison, biochemical characterization of kinase activity\",\n      \"journal\": \"Virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cross-species molecular analysis with functional kinase characterization, independently confirmed by multiple viral isolates\",\n      \"pmids\": [\"6301150\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"The human c-fps/fes product p92c-fes is a 92 kDa protein with tyrosine-specific kinase activity in vitro, capable of autophosphorylation and phosphorylation of exogenous substrate enolase; expression is largely confined to myeloid hematopoietic cells.\",\n      \"method\": \"Immunoprecipitation with anti-fps antiserum, in vitro kinase assay with enolase substrate, cell fractionation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct in vitro kinase assay with substrate phosphorylation, replicated across multiple labs and papers\",\n      \"pmids\": [\"2426571\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"NCP92 (p92c-fes) expression is restricted to cells of the monocyte/macrophage and granulocyte lineages in bone marrow and is not found in B-lymphocytic, T-lymphocytic, or erythroid cells; NCP92 has associated tyrosine kinase activity.\",\n      \"method\": \"Anti-peptide antibody immunoprecipitation, kinase activity assay, analysis of hematopoietic tumors by lineage\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal antibody-based detection with kinase assay, replicated in multiple cell types and independently confirmed\",\n      \"pmids\": [\"2986115\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1987,\n      \"finding\": \"The minimal catalytic domain of v-fps (P130gag-fps) begins at the predicted N-terminus of the ATP-binding site (residue 922); polypeptides containing ≥263 C-terminal residues are enzymatically active, autophosphorylate at physiological sites, and phosphorylate exogenous substrates (enolase, poly(glu,tyr)).\",\n      \"method\": \"Expression of trpE-v-fps hybrid proteins in E. coli, in vitro kinase assay, deletion mapping\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with systematic deletion mutagenesis defining catalytic domain boundaries, single lab but multiple constructs and orthogonal substrates\",\n      \"pmids\": [\"2449646\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"The c-fps gene product NCP98 (chicken) and its mammalian counterpart NCP92 show highest expression in macrophages and granulocytic cells; NCP98 kinase activity per cell correlates with peak granulopoiesis in bone marrow, spleen, and bursa.\",\n      \"method\": \"BSA density gradient fractionation of bone marrow cells, kinase activity measurement, complement-mediated lysis depletion\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct fractionation experiment with functional kinase readout, consistent with independent findings in human cells\",\n      \"pmids\": [\"2987674\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"The human c-fps/fes gene has a 13 kb genomic locus with 18 exons encoding a 93,390 Da protein (NCP92), deduced from nucleotide sequence; the gene architecture resembles the chicken c-fps locus.\",\n      \"method\": \"Nucleotide sequencing, Southern blot analysis, sequence deduction\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — complete gene structure determination, single study but comprehensive sequencing\",\n      \"pmids\": [\"4065096\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"Human p92c-fes expressed ectopically in Rat-2 fibroblasts is non-transforming despite ~50-fold overexpression; its kinase activity is restrained in vivo (no increase in cellular phosphotyrosine), even though the isolated protein is catalytically active in vitro. This in vivo restraint is lifted for v-fps/fes oncoproteins.\",\n      \"method\": \"Stable transfection, soft agar assay, immunoprecipitation/kinase assay, phosphotyrosine immunoblot, E. coli expression of kinase fragment\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — multiple orthogonal methods (transformation assay, in vivo phosphotyrosine, in vitro kinase), mechanistically informative negative result with positive in vitro control\",\n      \"pmids\": [\"3352601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1989,\n      \"finding\": \"FER (the human counterpart of rat flk) encodes a widely expressed 94 kDa protein-tyrosine kinase antigenically and structurally related to fps/fes; FER and fps/fes define a new subfamily of non-receptor PTKs sharing domain structure.\",\n      \"method\": \"cDNA cloning, sequencing, immunoblot with anti-fps antiserum, evolutionary conservation analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — structural and antigenic characterization establishing subfamily membership, single lab\",\n      \"pmids\": [\"2685575\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"A 13 kb genomic fragment of human c-fps/fes is sufficient for integration-independent, myeloid-specific expression in transgenic mice; expression is proportional to transgene copy number and recapitulates the endogenous myeloid expression pattern.\",\n      \"method\": \"Transgenic mouse generation, RNase protection, tissue distribution analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct in vivo transgenic experiment defining the cis-acting locus, single lab\",\n      \"pmids\": [\"2188092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"v-Fps induces Egr-1 promoter activation as a primary response (without protein synthesis); this responsiveness is mediated by serum response elements (SREs/CArG boxes) in the Egr-1 promoter, linking v-Fps tyrosine kinase activity to SRE-dependent transcription.\",\n      \"method\": \"Transient transfection with CAT reporter, deletion mutagenesis of Egr-1 promoter, co-transfection with v-Fps expression vector\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — promoter deletion mapping with functional reporter assay, single lab\",\n      \"pmids\": [\"1594452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"GM-CSF and IL-3 induce tyrosine phosphorylation and kinase activation of p92c-fes in TF-1 cells, and GM-CSF induces physical association between p92c-fes and the beta chain of the GM-CSF receptor, placing c-fps/fes downstream of these hematopoietic growth factor receptors.\",\n      \"method\": \"Immunoprecipitation, in vitro kinase assay, co-immunoprecipitation of p92c-fes with GM-CSF receptor beta chain\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and kinase activation assay, two orthogonal methods showing both physical association and functional activation\",\n      \"pmids\": [\"7682176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Erythropoietin (EPO) induces tyrosine phosphorylation and enhanced kinase activity of p92c-fes in human erythroleukemia TF-1 cells, implicating c-fps/fes in EPO receptor signaling.\",\n      \"method\": \"Immunoprecipitation, in vitro kinase assay, anti-phosphotyrosine immunoblot\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, immunoprecipitation and kinase assay, no direct receptor interaction demonstrated\",\n      \"pmids\": [\"7685196\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Activated (myristylated) Fps/Fes transforms Rat-2 fibroblasts and drives widespread hypervascularity progressing to multifocal hemangiomas in transgenic mice; fps/fes transcripts localize to endothelial cells of vascular tumors and normal blood vessels, indicating a direct role in angiogenesis regulation.\",\n      \"method\": \"Retroviral transformation assay, transgenic mouse model, in situ RNA hybridization, RNase protection\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (transformation, transgenic model, in situ hybridization) in one study, clear functional phenotype\",\n      \"pmids\": [\"7523858\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Spi-1/PU.1 and Spi-B transcription factors bind a site in the c-fes/c-fps promoter and activate c-fes transcription; Spi-1 binds this site in vivo in HL-60 cells, suggesting Spi-1 regulates myeloid-specific c-fes expression.\",\n      \"method\": \"PCR-mediated random site selection, in vitro binding/transcription assay, transfection in HeLa cells, gel shift with HL-60 nuclear extracts\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding plus in vivo chromatin/gel shift evidence, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"7624145\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"FES phosphorylates BCR on tyrosine residues upon co-expression in Sf-9 cells, forming a stable BCR-FES complex; this interaction involves the FES SH2 domain and a novel N-terminal BCR-binding domain (first 347 aa of FES). Tyrosine-phosphorylated BCR then associates with GRB-2/SOS, linking FES to RAS signaling. Deletion of the N-terminal BCR-binding domain from v-fps abolished transforming activity.\",\n      \"method\": \"Co-expression in Sf-9 insect cells, co-immunoprecipitation, deletion mutagenesis, transformation assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP with domain mapping mutagenesis and functional transformation readout, multiple orthogonal methods\",\n      \"pmids\": [\"7529874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Endothelial cells from hypervascular fps/fes transgenic mouse yolk sacs show a growth advantage and express high levels of the fps/fes tyrosine kinase, supporting a role in vasculogenesis and angiogenesis.\",\n      \"method\": \"Cell cloning from transgenic yolk sac, Southern blot genotyping, immunoblot for fps/fes expression, Matrigel tube formation assay\",\n      \"journal\": \"In vitro cellular & developmental biology. Animal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — cell biological characterization with functional endothelial assay, single lab\",\n      \"pmids\": [\"8792159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"fps-transformed fibroblasts show approximately 2-fold elevated concentrations of phosphatidate and diacylglycerol compared to controls, resulting from enhanced phospholipid turnover; ceramide concentrations are also elevated ~2.5-fold, linking fps tyrosine kinase activity to bioactive lipid second messenger pathways.\",\n      \"method\": \"Lipid extraction and quantification, phospholipid turnover assay, phosphatase/kinase activity measurements\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — biochemical measurements in transformed cells, indirect mechanistic link, single lab\",\n      \"pmids\": [\"9129148\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Fps/Fes-induced fibroblast transformation requires Ras, Rac, and Cdc42; ERK activation by v-Fps/Myr-Fes occurs exclusively downstream of Ras, while JNK activation requires both Ras and Rho-family GTPases (Rac and Cdc42), defining the small G protein/MAPK cascades through which Fps/Fes signals.\",\n      \"method\": \"Dominant-negative small G protein co-expression, soft agar transformation assay, ERK and JNK kinase activity measurements\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with dominant-negatives plus direct kinase assays, multiple pathways dissected, single lab\",\n      \"pmids\": [\"9593727\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"v-Fps induces tyrosine phosphorylation and activation of the PDGFbeta receptor within minutes of kinase activation; sustained v-Fps expression causes >100-fold downregulation of PDGF receptor protein. Kinase activity of v-Fps is required for both PDGF receptor phosphorylation and downregulation. A kinase-inactive PDGF receptor cannot mediate transformation even when phosphorylated by v-Fps.\",\n      \"method\": \"Immunoprecipitation/kinase assay, immunoblot, soft agar colony formation assay, kinase-inactive PDGF receptor mutant co-expression\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods with mutagenesis validation, single lab\",\n      \"pmids\": [\"9620549\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Kinase-inactivating missense mutation in murine fps/fes results in dramatically reduced Stat3 and Stat5A tyrosine phosphorylation in response to GM-CSF (but not IL-3 or IL-6) in bone marrow-derived macrophages, and reduced LPS-induced Erk1/2 activation, demonstrating a non-redundant role for Fps/Fes kinase activity in GM-CSF receptor signaling.\",\n      \"method\": \"Knock-in mouse model, flow cytometry, signaling analysis by immunoblot, bone marrow colony-forming assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — defined kinase-inactivating knock-in with specific signaling readouts, replicated independently\",\n      \"pmids\": [\"10523632\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Fps/Fes localizes to cytoplasmic vesicles and a perinuclear Golgi region (colocalizing with TGN38), and also colocalizes with Rab proteins involved in both endocytosis (Rab5B, Rab7) and exocytosis (Rab1A, Rab3A); this localization is disrupted by brefeldin A. Fer is diffusely cytoplasmic. This distinct vesicular localization suggests a role for Fps/Fes in vesicular trafficking.\",\n      \"method\": \"GFP fusion proteins, confocal fluorescence microscopy, colocalization with TGN38 and Rab markers, brefeldin A perturbation\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct live-cell imaging with multiple colocalization markers and pharmacological perturbation, single lab\",\n      \"pmids\": [\"11339827\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Fps/Fes-null mice are more sensitive to LPS-induced endotoxicity; fps/fes kinase is involved in but not required for myelopoiesis; phenotypes are rescued by fps/fes transgene. Fps/Fes-null macrophages show no defects in GM-CSF-, IL-6-, or IL-3-induced Stat3/Stat5A activation or LPS-induced IκB degradation, p38, JNK, ERK, or Akt activation.\",\n      \"method\": \"Fps/fes-null mouse model, LPS challenge, flow cytometry, signaling analysis by immunoblot, transgene rescue\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — null mouse with transgene rescue, comprehensive signaling panel, multiple orthogonal readouts\",\n      \"pmids\": [\"11909942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Fes/Fps tyrosine kinase interacts with plexinA1 (PlexA1) and phosphorylates PlexA1 on tyrosine; neuropilin-1 (NP-1) attenuates this interaction in resting conditions but semaphorin3A (Sema3A) enhances Fes-PlexA1 association and Fes-mediated phosphorylation of PlexA1, CRAM, and CRMP2. Fes kinase-negative mutants suppress Sema3A-induced growth cone collapse, placing Fes in the Sema3A signaling pathway.\",\n      \"method\": \"Co-immunoprecipitation in COS-7 cells, cell morphology assay, dominant-negative kinase mutant, DRG neuron growth cone collapse assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP with dominant-negative mutagenesis and two functional readouts (cell contraction, growth cone collapse), single lab but multiple orthogonal methods\",\n      \"pmids\": [\"12093729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Fps/Fes and Fer are expressed in platelets and are activated following collagen/CRP stimulation (GPVI pathway); Fer is also activated by thrombin/PAR4. Fps/Fes-null platelets show increased collagen-induced aggregation and elevated P-selectin surface expression; Fer-deficient platelets disaggregate more rapidly in response to ADP, demonstrating roles for these kinases in platelet aggregation regulation.\",\n      \"method\": \"Immunoprecipitation/kinase assay from platelet lysates, platelet aggregometry, P-selectin flow cytometry, targeted knockout mouse models\",\n      \"journal\": \"Journal of thrombosis and haemostasis : JTH\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple functional assays with knockout mouse models, single lab\",\n      \"pmids\": [\"12871378\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Fes tyrosine kinase associates with microtubules and promotes microtubule bundling in a kinase-dependent manner; the FCH (Fes/CIP4 homology) domain of Fes colocalizes with gamma-tubulin at microtubule nucleation sites. FCH-deleted Fes blocks centrosome formation, and Fes-deficient mouse embryonic fibroblasts display aberrant microtubule nucleation and centrosome structure.\",\n      \"method\": \"Confocal microscopy, co-localization with gamma-tubulin, microtubule regeneration assay, FCH deletion mutants, Fes-deficient MEFs\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct imaging with domain mutagenesis and knockout MEF validation, single lab\",\n      \"pmids\": [\"14551201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Mice lacking both Fps and Fer kinase activities are viable but show reduced fertility, elevated circulating neutrophils/erythrocytes/platelets, reduced bone marrow cellularity, and elevated CD11b(hi)Ly-6G(lo) myeloid cells, demonstrating functional redundancy between Fps and Fer in regulating hematopoiesis.\",\n      \"method\": \"Compound knock-in mouse model, flow cytometry, peripheral blood counts, bone marrow colony-forming assays\",\n      \"journal\": \"Experimental hematology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — double kinase-inactivating knock-in model with comprehensive hematopoietic analysis, single lab\",\n      \"pmids\": [\"12901971\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Three of four somatic fps/fes kinase domain mutations found in colorectal cancers result in kinase inactivation, not activation; a fourth compromises in vivo activity. Tumor onset is accelerated in mice with fps/fes null or kinase-inactivating mutations in a breast cancer model, and restored by fps/fes transgene, suggesting a tumor suppressor role for Fps/Fes in epithelial cells.\",\n      \"method\": \"Biochemical kinase assays of mutant proteins, structural modeling, transgenic/knock-in mouse tumor model, tumor onset kinetics\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro kinase assay of cancer-derived mutants combined with in vivo mouse tumor model and transgene rescue, multiple orthogonal approaches\",\n      \"pmids\": [\"15867340\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Fps/Fes-null macrophages display prolonged LPS-induced IκBα degradation, increased NF-κB p65 phosphorylation, increased TNF-α production, and defective TLR4 internalization compared to wild-type macrophages. This provides a mechanistic basis for enhanced endotoxin sensitivity of Fps/Fes-null mice: Fps/Fes modulates innate immune responses partly by regulating TLR4 internalization.\",\n      \"method\": \"Fps/fes-null macrophage culture, ELISA for TNF-α, immunoblot for IκBα and phospho-p65, TLR4 internalization assay\",\n      \"journal\": \"Journal of leukocyte biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — null macrophages with multiple orthogonal signaling readouts and defined phenotypic mechanism, single lab\",\n      \"pmids\": [\"16959897\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"FcεRI aggregation in mast cells leads to increased Fer/Fps kinase activities in a Lyn-dependent manner (independent of Syk, Fyn, and Gab2). Activated Fer/Fps phosphorylate PECAM-1 ITIMs and Tyr700 in vitro and in transfected cells. Mast cells devoid of Fer/Fps kinase activities show reduced PECAM-1 phosphorylation and exaggerated degranulation at low antigen doses.\",\n      \"method\": \"Kinase activity assay, in vitro phosphorylation of PECAM-1, transfected cell phosphorylation, mast cells from kinase-deficient mice, degranulation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — direct in vitro substrate phosphorylation combined with genetic mouse models and defined cellular phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"16731527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"FES is phosphorylated on tyrosine residues in cells harboring KIT(D816V) in a KIT-dependent manner; RNAi-mediated reduction of FES expression decreases cell proliferation in human and murine cells with KIT(D816V) or KIT(D814Y), and the growth defect is rescued by GM-CSF. FES knockdown alters signaling downstream of KIT(D816V), identifying FES as an essential effector of oncogenic KIT.\",\n      \"method\": \"RNAi knockdown, proliferation assay, phosphotyrosine immunoblot, GM-CSF rescue, signaling analysis\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNAi knockdown with functional rescue, specific signaling analysis, comparison with FER knockdown, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"17595334\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Both FES and FER are activated in AML blasts and cell lines in a FLT3-dependent manner; RNAi knockdown of FES or FER inhibits proliferation downstream of FLT3-ITD, with FER required for cell cycle transitions and FES necessary for cell survival, demonstrating non-redundant functions of FES and FER downstream of oncogenic FLT3.\",\n      \"method\": \"RNAi knockdown, proliferation/cell cycle/survival assays in AML cell lines, activation status by immunoprecipitation/kinase assay\",\n      \"journal\": \"Leukemia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNAi with multiple functional readouts distinguishing FES vs FER roles, single lab\",\n      \"pmids\": [\"20111072\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CRISPR-engineered monocytic cell lines with 15q26.1 CAD risk genotype have reduced FES expression. FES knockdown promotes migration of monocytes and vascular smooth muscle cells and alters phosphorylation of migration-regulating proteins (phosphoproteomics). Fes knockout in ApoE-deficient mice increases atherosclerotic plaque size and monocyte/macrophage and smooth muscle cell content, identifying FES as a protective factor against atherosclerosis.\",\n      \"method\": \"CRISPR genome editing, siRNA knockdown, phosphoproteomics, migration assays, scRNA-seq, Fes knockout in ApoE-deficient mouse atherosclerosis model\",\n      \"journal\": \"Circulation research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods including CRISPR editing, phosphoproteomics, and in vivo mouse model with defined phenotype\",\n      \"pmids\": [\"36321446\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FES (c-Fps/Fes) is a cytoplasmic non-receptor protein-tyrosine kinase that is activated downstream of hematopoietic growth factor receptors (GM-CSF, IL-3, EPO) and immune receptors (FcεRI, KIT, FLT3), where it phosphorylates substrates including BCR, PECAM-1, PlexA1, CRMP2, and the PDGFβ receptor; its kinase activity is restrained in normal cells through regulatory interactions but activated in oncogenic contexts; it signals through Ras/Rac/Cdc42 to ERK and JNK, regulates TLR4 internalization to limit innate immune responses, localizes to Golgi/vesicular compartments suggesting a role in vesicular trafficking, and promotes microtubule nucleation and bundling through its FCH domain, with overall roles in myeloid differentiation, angiogenesis, platelet aggregation, semaphorin signaling, and atherosclerosis suppression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FES (c-Fps/Fes) is a cytoplasmic non-receptor protein-tyrosine kinase expressed predominantly in myeloid hematopoietic cells (monocyte/macrophage and granulocyte lineages) that acts as a signaling effector downstream of hematopoietic growth factor and immune receptors [#3, #4]. The mature protein autophosphorylates and phosphorylates exogenous tyrosine substrates in vitro, and its catalytic activity resides in a C-terminal kinase domain while its SH2 domain selects Group I phosphopeptide motifs (phospho-Tyr-hydrophilic-hydrophilic-hydrophobic) [#0, #5]. Although intrinsically active in vitro, FES kinase activity is restrained in normal cells, and this restraint is relieved in oncogenic v-fps/fes forms that drive cellular transformation [#1, #8]. FES is activated by GM-CSF, IL-3, and EPO and physically associates with the GM-CSF receptor beta chain, with kinase-inactivating knock-in mice revealing a non-redundant requirement for FES in GM-CSF-induced Stat3/Stat5A phosphorylation [#12, #21]. Downstream, FES phosphorylates BCR to nucleate a GRB2/SOS complex and signals through Ras to ERK and through Ras plus Rac/Cdc42 to JNK [#16, #19]. FES also phosphorylates the PDGFbeta receptor, plexinA1/CRMP2 in semaphorin3A-induced growth cone collapse, and PECAM-1 ITIMs downstream of FcepsilonRI to restrain mast cell degranulation [#20, #24, #30]. In innate immunity it limits TLR4 signaling by promoting receptor internalization, accounting for endotoxin hypersensitivity of FES-null mice [#23, #29]. Beyond signaling, FES localizes to Golgi and Rab-marked vesicular compartments and, via its FCH domain, associates with microtubules and gamma-tubulin to promote microtubule bundling and centrosomal nucleation [#22, #26]. FES is an essential effector of oncogenic KIT and FLT3-ITD in leukemic cells, yet functions as a tumor suppressor in epithelial cancers and protects against atherosclerosis by restraining monocyte and smooth muscle cell migration [#28, #31, #32, #33].\",\n  \"teleology\": [\n    {\n      \"year\": 1983,\n      \"claim\": \"Established that the transforming activity of the fps/fes oncogene resides in a tyrosine kinase encoded by a single conserved cellular locus, defining the gene's core biochemical identity.\",\n      \"evidence\": \"Cloned viral DNA transfection, immunoprecipitation/in vitro kinase assay, tumor induction, and cross-species molecular hybridization\",\n      \"pmids\": [\"6605429\", \"6301150\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define the cellular substrates or physiological regulators of the normal c-fps/fes product\", \"Transformation readouts used viral oncogene, not the proto-oncogene\"]\n    },\n    {\n      \"year\": 1985,\n      \"claim\": \"Defined the human proto-oncogene product p92c-fes as a myeloid-restricted tyrosine kinase, linking the kinase to a specific hematopoietic lineage.\",\n      \"evidence\": \"Anti-peptide antibody immunoprecipitation, in vitro kinase/enolase phosphorylation, lineage analysis of hematopoietic cells and gene structure determination\",\n      \"pmids\": [\"2426571\", \"2986115\", \"2987674\", \"4065096\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify activating receptors or physiological substrates\", \"Mechanism of lineage-restricted expression unresolved at this stage\"]\n    },\n    {\n      \"year\": 1987,\n      \"claim\": \"Mapped the minimal catalytic domain, showing the C-terminal kinase region alone is sufficient for autophosphorylation and substrate phosphorylation.\",\n      \"evidence\": \"E. coli expression of trpE-v-fps deletion constructs with in vitro kinase assays\",\n      \"pmids\": [\"2449646\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Used viral v-fps, not the regulated cellular protein\", \"Did not address how N-terminal/SH2 regions regulate activity in cells\"]\n    },\n    {\n      \"year\": 1988,\n      \"claim\": \"Revealed that the normal kinase is intrinsically active yet held in check in vivo, distinguishing the proto-oncogene from its transforming viral counterpart.\",\n      \"evidence\": \"Stable overexpression in Rat-2 fibroblasts with soft agar, in vivo phosphotyrosine immunoblot, and in vitro kinase controls\",\n      \"pmids\": [\"3352601\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of the in vivo restraint not defined\", \"Did not identify the cellular context where restraint is physiologically relieved\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Placed c-fps/fes downstream of hematopoietic cytokine receptors by demonstrating receptor-induced activation and physical receptor association.\",\n      \"evidence\": \"Immunoprecipitation/kinase assay and co-IP with GM-CSF receptor beta chain in TF-1 cells; EPO-induced activation\",\n      \"pmids\": [\"7682176\", \"7685196\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"EPO receptor interaction not demonstrated directly\", \"Downstream substrates of receptor-activated FES not yet defined\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Identified BCR as a FES substrate that couples the kinase to Ras signaling and showed the N-terminal BCR-binding domain is required for transformation.\",\n      \"evidence\": \"Co-expression in Sf-9 cells, co-IP, SH2/domain deletion mutagenesis, and transformation assay\",\n      \"pmids\": [\"7529874\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Interaction mapped in heterologous insect cells\", \"Physiological role of BCR-FES complex in myeloid cells not established\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Dissected the GTPase/MAPK architecture downstream of FES, separating Ras-dependent ERK activation from Ras/Rac/Cdc42-dependent JNK activation.\",\n      \"evidence\": \"Dominant-negative small G protein co-expression with soft agar and ERK/JNK kinase assays; PDGFbeta receptor phosphorylation/downregulation experiments\",\n      \"pmids\": [\"9593727\", \"9620549\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Used activated Fps/Fes transformation context, not normal signaling\", \"Direct linkage between FES substrates and GTPase activation incompletely defined\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Demonstrated a non-redundant, kinase-dependent requirement for FES in GM-CSF receptor signaling in vivo via a knock-in mouse.\",\n      \"evidence\": \"Kinase-inactivating knock-in mouse, immunoblot of Stat3/Stat5A and Erk1/2 in bone marrow-derived macrophages\",\n      \"pmids\": [\"10523632\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specificity to GM-CSF over IL-3/IL-6 mechanistically unexplained\", \"Direct STAT phosphorylation by FES not shown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Localized FES to Golgi and Rab-marked vesicular compartments, implicating it in vesicular trafficking and distinguishing it from diffusely cytoplasmic Fer.\",\n      \"evidence\": \"GFP-fusion confocal imaging, colocalization with TGN38 and Rab markers, brefeldin A perturbation\",\n      \"pmids\": [\"11339827\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of vesicular localization for trafficking not tested\", \"Single-lab imaging without orthogonal biochemical fractionation\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Extended FES function beyond hematopoiesis into innate immunity and axon guidance, defining roles in endotoxin response and semaphorin signaling.\",\n      \"evidence\": \"Fps/fes-null mice with LPS challenge and signaling panels; co-IP and growth cone collapse assays for the PlexA1/Sema3A pathway\",\n      \"pmids\": [\"11909942\", \"12093729\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism connecting FES to endotoxin sensitivity not yet defined in 2002\", \"PlexA1 interaction characterized in COS-7 overexpression\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Uncovered cytoskeletal and platelet functions and established functional redundancy with Fer in hematopoiesis.\",\n      \"evidence\": \"Microtubule bundling/gamma-tubulin colocalization with FCH deletion in MEFs; platelet aggregometry and P-selectin assays; compound Fps/Fer kinase-inactivating knock-in mice\",\n      \"pmids\": [\"14551201\", \"12871378\", \"12901971\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Microtubule and platelet substrates of FES not identified\", \"Mechanism of FCH-mediated microtubule nucleation incompletely defined\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Revealed a context-dependent tumor suppressor role in epithelial cancers, with cancer-associated mutations inactivating rather than activating the kinase.\",\n      \"evidence\": \"Biochemical kinase assays of colorectal cancer-derived mutants, structural modeling, breast cancer mouse model with null/knock-in alleles and transgene rescue\",\n      \"pmids\": [\"15867340\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Epithelial substrates mediating tumor suppression not identified\", \"Reconciliation of suppressor versus oncogenic roles mechanistically open\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Provided mechanistic basis for FES control of innate immunity and immune-receptor signaling via TLR4 internalization and PECAM-1 phosphorylation.\",\n      \"evidence\": \"Fps/fes-null macrophages with TLR4 internalization assays, NF-kB readouts; FcepsilonRI-activated mast cells with in vitro PECAM-1 phosphorylation and degranulation assays\",\n      \"pmids\": [\"16959897\", \"16731527\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How FES promotes TLR4 internalization at the molecular level unresolved\", \"Lyn-to-FES activation step in mast cells not fully mapped\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Established FES (with FER) as a non-redundant effector of oncogenic receptor tyrosine kinases in leukemia.\",\n      \"evidence\": \"RNAi knockdown with proliferation/survival/cell-cycle assays in KIT(D816V) and FLT3-ITD cells, with kinase activation status and GM-CSF rescue\",\n      \"pmids\": [\"17595334\", \"20111072\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct FES substrates downstream of KIT/FLT3 not defined\", \"Whether FES is directly phosphorylated by these receptors versus indirectly activated unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked a human CAD risk locus to reduced FES expression and a protective role against atherosclerosis through restraint of cell migration.\",\n      \"evidence\": \"CRISPR genotype editing, siRNA, phosphoproteomics, migration assays, scRNA-seq, and Fes knockout in ApoE-deficient atherosclerosis model\",\n      \"pmids\": [\"36321446\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific FES substrates governing migration not pinpointed\", \"Cell-type-specific contributions of monocyte versus smooth muscle FES not separated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular basis for the in vivo restraint of FES kinase activity and how the same kinase functions as both an oncogenic effector and a tumor/atherosclerosis suppressor across cell types remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying structural mechanism for context-dependent activation/restraint\", \"Physiological direct substrates in epithelial and vascular settings not catalogued\", \"Vesicular and microtubule functions not connected to a defined signaling output\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [3, 5, 16, 20, 24, 30]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [26]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [22]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [22]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [26]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [26]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [12, 19, 24]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [23, 29, 30]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [28, 31, 32, 33]},\n      {\"term_id\": \"R-HSA-109582\", \"supporting_discovery_ids\": [25]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"BCR\", \"PLEXINA1\", \"PECAM1\", \"PDGFRB\", \"CSF2RB\", \"KIT\", \"FLT3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":9,"faith_total":9,"faith_pct":100.0}}