{"gene":"CD40","run_date":"2026-04-28T17:28:52","timeline":{"discoveries":[{"year":1986,"finding":"CD40 (Bp50) is a 50-kDa cell-surface molecule on all B cells that delivers activation signals promoting B-cell progression through the cell cycle; anti-Bp50 monoclonal antibody augments proliferation of activated B cells but does not activate resting B cells alone, distinguishing it functionally from Bp35 (surface Ig).","method":"Monoclonal antibody stimulation assays on purified tonsillar B cells; cell-cycle analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — clean functional dissection with defined phenotypic readout, foundational paper replicated extensively","pmids":["3487090"],"is_preprint":false},{"year":1989,"finding":"CD40 (Bp50/CDw40) encodes a B-lymphocyte activation molecule whose predicted sequence shares extensive homology with the nerve growth factor receptor, placing it in the TNF receptor superfamily; its mRNA is induced by gamma-interferon in B cells and carcinomas.","method":"cDNA cloning, sequence analysis with transition matrix method, Northern blot","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 — original molecular cloning and sequence analysis, foundational structural finding","pmids":["2475341"],"is_preprint":false},{"year":1990,"finding":"IL-6 induces phosphorylation of CD40 in B cells through a mechanism requiring an intact CD40 cytoplasmic tail (including threonine-234), and conversely, CD40 ligation induces IL-6 production; this cross-talk requires functional CD40 but CD40 is not an IL-6 receptor.","method":"Mutagenesis of CD40 cytoplasmic tail (tailless and T234A mutants), growth inhibition assays, phosphorylation assays in M12 transformants","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 — site-directed mutagenesis with functional readout in defined cell line, single lab","pmids":["1696597"],"is_preprint":false},{"year":1994,"finding":"CD40 is a 45–50 kDa glycoprotein of 277 amino acids; its gene maps to human chromosome 20q11.2–q13.2. CD40 ligation drives B-cell proliferation, isotype switching (to IgE with IL-4/IL-13, to IgG3/IgG1/IgA1 with IL-10), and generation of long-term B-cell lines. Deficiency of CD40L underlies X-linked hyper-IgM syndrome.","method":"Biochemical characterization, gene mapping, B-cell culture assays with recombinant CD40L and cytokines","journal":"Annual review of immunology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods, replicated across labs, comprehensive review synthesizing original experimental work","pmids":["7516669"],"is_preprint":false},{"year":1994,"finding":"gp39 (CD40L)–CD40 interactions are required for germinal center formation and generation of antigen-specific memory B cells in vivo; anti-gp39 antibody treatment completely abolished splenic germinal centers and blocked memory B-cell generation in adoptive transfer experiments.","method":"In vivo antibody blockade, immunohistochemistry, adoptive transfer experiments in mice","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — genetic/antibody epistasis with defined in vivo phenotype, replicated","pmids":["7516405"],"is_preprint":false},{"year":1994,"finding":"Cyclosporin A (CsA) inhibits CD40L expression on T lymphocytes through calcineurin-dependent signaling: optimal CD40L expression requires protein kinase C activation and a rise in intracellular calcium; CsA inhibited IL-4-driven, CD40L-dependent IgE isotype switching.","method":"CsA analog dose-response correlating with calcineurin inhibition, T-cell activation assays, IgE switching assay","journal":"The Journal of clinical investigation","confidence":"Medium","confidence_rationale":"Tier 2 — pharmacological dissection with calcineurin correlation, single lab","pmids":["7907604"],"is_preprint":false},{"year":1995,"finding":"TRAF2 (via CRAF1) directly binds the CD40 cytoplasmic tail through a shared TRAF-C domain that is necessary and sufficient for both CD40 binding and homodimerization; overexpression of a truncated CRAF1 inhibited CD40-mediated upregulation of CD23, identifying TRAF proteins as CD40 signal transducers.","method":"Yeast two-hybrid screen, dominant-negative overexpression, CD23 upregulation assay","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 — yeast two-hybrid plus dominant-negative functional validation, foundational discovery replicated by multiple labs","pmids":["7533327"],"is_preprint":false},{"year":1995,"finding":"TRAF2-mediated NF-κB activation is a common signaling output of TNF-R2 and CD40; overexpression of TRAF2 is sufficient to induce NF-κB activation, and a dominant-negative TRAF2 (lacking the RING finger domain) blocks NF-κB activation by both receptors.","method":"Overexpression and dominant-negative experiments, NF-κB reporter assay","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 — dominant-negative epistasis with defined molecular readout, replicated","pmids":["7544915"],"is_preprint":false},{"year":1995,"finding":"CD40 is expressed on vascular endothelial cells and is upregulated by inflammatory agents; ligation by soluble gp39 (CD40L) activates endothelial cells to express E-selectin, ICAM-1, and augments VCAM-1 expression, promoting leukocyte adhesion.","method":"Flow cytometry, soluble recombinant CD40L stimulation, antibody blockade, adhesion assays, immunohistochemistry of inflammatory skin tissue","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods with functional readout, replicated","pmids":["7540655"],"is_preprint":false},{"year":1995,"finding":"CD40 is expressed on human umbilical vein endothelial cells and upregulated ~3-fold by TNF, IL-1, IFN-β, or IFN-γ; CD40 ligation by trimeric CD40L increases expression of E-selectin, VCAM-1, and ICAM-1 on endothelial cells.","method":"Flow cytometry, cytokine stimulation, recombinant trimeric CD40L ligation, adhesion molecule quantitation","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — multiple cytokines tested, defined molecular readouts, replicated","pmids":["7538666"],"is_preprint":false},{"year":1996,"finding":"CD40L-dependent T cell activation occurs through CD40 signaling on antigen-presenting cells that upregulates B7 costimulatory molecules (B7.2); reconstitution of CD40L-deficient mice with an activating anti-CD40 antibody restored both cellular and humoral immunity, which was then blocked by anti-B7 antibodies.","method":"CD40L-deficient mouse model, anti-CD40 agonist antibody reconstitution, anti-B7 blockade","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 — genetic reconstitution epistasis experiment with defined molecular pathway","pmids":["8791591"],"is_preprint":false},{"year":1996,"finding":"CD40L (gp39)-positive helper T cells are co-localized with CD40-bearing monocytes/macrophages in active multiple sclerosis lesions; anti-CD40L monoclonal antibody prevented and treated experimental allergic encephalomyelitis (EAE) in mice, identifying CD40-CD40L as a functional mediator of CNS inflammation.","method":"Immunohistochemistry of MS brain sections, in vivo antibody blockade in EAE mouse model","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — combined human tissue analysis and functional in vivo intervention","pmids":["8637903"],"is_preprint":false},{"year":1996,"finding":"A novel protein TRAF5 (originally identified as CRAF1 relative) binds the CD40 cytoplasmic tail; TRAF5-deficient B cells show defects in proliferation and upregulation of CD23, CD54, CD80, CD86, and Fas in response to CD40 stimulation, and reduced Ig production with IL-4.","method":"Gene targeting (TRAF5-/- mice), B-cell stimulation assays, surface molecule expression analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — genetic knockout with multiple defined phenotypic readouts","pmids":["10449775"],"is_preprint":false},{"year":1996,"finding":"CD40 on dendritic cells mediates T-lymphocyte activation in allogeneic mixed leukocyte reactions; cross-linking of CD40 on DCs markedly augments CD80 and CD86 expression, and CD40-CD40L co-stimulation of DCs has both CD80/CD86-dependent and -independent components.","method":"CD40-Ig fusion protein blockade, CD40L trimer cross-linking, MLR assay, flow cytometry","journal":"European journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 — functional blockade and stimulation assays, single lab","pmids":["8647193"],"is_preprint":false},{"year":1997,"finding":"Platelets express CD40L within seconds of activation in vitro and during thrombus formation in vivo; platelet CD40L induces endothelial cells to secrete chemokines and express adhesion molecules, initiating an inflammatory response at sites of vessel injury.","method":"Flow cytometry, immunofluorescence, intravital microscopy, endothelial cell stimulation assay","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — in vitro and in vivo demonstration, multiple orthogonal methods, highly cited","pmids":["9468137"],"is_preprint":false},{"year":1997,"finding":"IL-2-activated NK cells express CD40L and can kill CD40-expressing target cells through a CD40-dependent activation pathway; CD40L cross-linking on NK cells induces redirected cytolysis, and this pathway can be downregulated by MHC class I molecules on target cells.","method":"NK cell killing assays with CD40-transfected targets, anti-CD40 antibody blockade, CD40L cross-linking with redirected cytolysis","journal":"The Journal of experimental medicine","confidence":"Medium","confidence_rationale":"Tier 2 — functional assays with antibody blockade and genetic controls, single lab","pmids":["9182676"],"is_preprint":false},{"year":1997,"finding":"CD40L is constitutively expressed by human vascular endothelial cells, smooth muscle cells, and macrophages (not only activated T cells); these cell types co-express CD40 and CD40L in atherosclerotic lesions, enabling autocrine/paracrine signaling. CD40L on SMCs and macrophages is biologically active, inducing B7.2 on B cells and proinflammatory cytokines in SMCs.","method":"RT-PCR, immunohistochemistry, flow cytometry, B7.2 induction assay, cytokine ELISA","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — multiple cell types, multiple methods, in vitro and in situ validation","pmids":["9050882"],"is_preprint":false},{"year":1998,"finding":"CD40 signaling through CD40L-CD40 interactions is required for CTL priming by cross-presentation; signaling through CD40 on antigen-presenting cells can substitute for CD4+ T helper cell help in generating CD8+ cytotoxic T-cell responses.","method":"CD40L-deficient mice, agonistic anti-CD40 antibody reconstitution, CTL priming assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — genetic KO plus antibody reconstitution epistasis, highly cited and replicated","pmids":["9624004"],"is_preprint":false},{"year":1998,"finding":"Anti-CD40L antibody treatment reduced atherosclerotic lesion size by 59% and lipid content by 79% in hyperlipidemic LDL-receptor-deficient mice, with significant decreases in macrophages (64%), T lymphocytes (70%), and VCAM-1 expression, establishing a causal role for CD40 signaling in atherogenesis in vivo.","method":"In vivo antibody blockade in LDL-receptor KO mice on high-cholesterol diet, morphometric analysis, immunohistochemistry","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic/pharmacological intervention with quantified molecular and cellular phenotypes, highly cited","pmids":["9671306"],"is_preprint":false},{"year":1996,"finding":"TRAF6 binds a distinct region of the CD40 cytoplasmic domain (residues 230–245) that is separate from the TRAF2/3/5 binding site (residues 246–269); TRAF6 overexpression activates NF-κB, and its TRAF-C domain suppresses NF-κB activation triggered by CD40 lacking residues 246–277, indicating TRAF6 mediates a distinct CD40 signaling pathway.","method":"Yeast two-hybrid, deletion analysis, NF-κB reporter assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — deletion mapping plus functional NF-κB assay, replicated by structural studies","pmids":["8910514"],"is_preprint":false},{"year":1998,"finding":"RIP2 (a novel serine/threonine kinase with a CARD domain) is a component of the CD40 signaling complex; RIP2 overexpression activates NF-κB (requiring intact kinase domain plus CARD) and induces cell death (via CARD alone); RIP2 interacts with TRAF1, TRAF5, and TRAF6 but not TRAF2/3/4.","method":"Co-immunoprecipitation, overexpression, mutational analysis, NF-κB reporter assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus mutagenesis with functional readout, single lab","pmids":["9642260"],"is_preprint":false},{"year":1999,"finding":"Crystal structure (2.4 Å) of the TRAF2 receptor-binding fragment complexed with a CD40 cytoplasmic domain peptide reveals that TRAF2 forms a mushroom-shaped homotrimer; the CD40 peptide binds in an extended conformation with every side chain contacting a complementary groove on each TRAF monomer rim; spacing of CD40 binding sites on the TRAF2 trimer supports a signaling mechanism in which trimeric ligands pre-organize receptors to simultaneously engage three TRAF monomers.","method":"X-ray crystallography at 2.4 Å resolution","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — atomic resolution crystal structure of CD40-TRAF2 complex","pmids":["10411888"],"is_preprint":false},{"year":2001,"finding":"CD40 pre-mRNA is alternatively spliced to generate multiple isoforms; expression shifts from signal-transducible CD40 mRNA early in macrophage/DC activation to signal-nontransducible isoforms (accounting for ~50% of CD40 mRNA) at 24 h; three alternative isoforms can disable CD40 signaling, with the major isoform lacking the membrane-associated endodomain reducing full-length CD40 on the cell surface.","method":"RT-PCR, IL-12 p40 reporter assay for CD40 signaling, transfection of isoforms in macrophages and DCs","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 — functional isoform analysis with reporter readout, single lab","pmids":["11172023"],"is_preprint":false},{"year":2001,"finding":"CD40 mRNA and protein are expressed by neuronal cells and are upregulated during differentiation; CD40 ligation in neuronal cells activates p44/42 MAPK and opposes JNK phosphorylation induced by NGF withdrawal, protecting neurons from injury; adult CD40-deficient mice show neuronal dysfunction with decreased neurofilament isoforms, reduced Bcl-xL:Bax ratio, and increased DNA fragmentation.","method":"RT-PCR, Western blot, immunofluorescence, MAPK activation assays, JNK assay, CD40 KO mouse analysis","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 — multiple methods in vitro and KO phenotype in vivo, single lab","pmids":["11847112"],"is_preprint":false},{"year":2001,"finding":"AKNA, an AT-hook transcription factor, directly binds A/T-rich regulatory elements in the promoters of both CD40 and CD40L and coordinately regulates their expression; AKNA is a nuclear protein with PEST motifs expressed by germinal center B lymphocytes, T cells, NK cells, and DCs.","method":"Promoter binding assay, transfection, reporter gene assay, nuclear localization studies","journal":"Nature","confidence":"Medium","confidence_rationale":"Tier 2 — direct promoter binding demonstrated, coordinate regulation shown, single lab","pmids":["11268217"],"is_preprint":false},{"year":2001,"finding":"Act1 is a novel adaptor molecule that negatively regulates CD40 and BAFFR signaling; Act1-deficient B cells show significantly increased survival with stronger IκB phosphorylation, enhanced p100/p52 NF-κB2 processing, and augmented JNK, ERK, and p38 activation following CD40 stimulation; the B-cell phenotype in Act1-KO mice was largely rescued by double KO with CD40.","method":"Genetic knockout, double-knockout epistasis, B-cell signaling assays (NF-κB, MAPK pathways)","journal":"Immunity","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with multiple orthogonal signaling readouts","pmids":["15485634"],"is_preprint":false},{"year":2002,"finding":"Crystal structures of TRAF6 alone and in complex with TRAF6-binding peptides from CD40 (and TRANCE-R) reveal a Pro-X-Glu-X-X-(aromatic/acidic) binding motif that differs fundamentally from TRAF2 peptide recognition (40° difference in bound peptide direction); cell-permeable peptides with this motif inhibit TRAF6 signaling.","method":"X-ray crystallography of TRAF6-CD40 peptide complex, cell-permeable peptide inhibition assay","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — atomic resolution crystal structure defining distinct CD40-TRAF6 interaction mechanism","pmids":["12140561"],"is_preprint":false},{"year":2001,"finding":"Soluble trimeric CD40 cytoplasmic domain constructs associate in complexes containing TRAF2, TRAF3, TRAF5, TRAF6, and c-IAP1; c-IAP1 association with the CD40 complex is indirect and dependent on an intact TRAF1/2/3 binding site; trimeric (but not monomeric) CD40 cytoplasmic domain is sufficient to activate NF-κB, indicating receptor trimerization is the minimal signaling unit.","method":"Soluble and myristoylated multimeric CD40 cytoplasmic domain constructs, immunoprecipitation, NF-κB reporter assay, point mutation analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — reconstitution of signaling complexes with mutagenesis and functional readout","pmids":["11562359"],"is_preprint":false},{"year":2003,"finding":"CD40 ligation on human endothelial cells induces expression of multiple angiogenesis factors including FGF-2, Flt-1, and Flt-4 in vitro; injection of CD40L-expressing fibroblasts into human skin grafts on SCID mice elicited angiogenesis factor expression and marked angiogenesis in vivo, which was abrogated by anti-VEGF, establishing a VEGF-dependent proangiogenic function of CD40 ligation.","method":"Anti-CD40 antibody stimulation of cultured ECs, in vivo SCID mouse skin graft model with CD40L-transfected fibroblasts, anti-VEGF blockade","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro and in vivo experiments with antibody blockade, single lab","pmids":["12874247"],"is_preprint":false},{"year":2003,"finding":"CD40 ligation stimulates antigen processing by B cells, enhancing MHC class II-restricted antigen presentation to T-cell hybrids; CD40 acts at an intracellular processing step (not peptide presentation per se) and independently of effects on B7, LFA-1, or CD23 expression or B-cell proliferation.","method":"B-cell/T-cell hybrid co-culture assay, recombinant CD40L-expressing insect cells, anti-CD40 mAb, peptide presentation controls","journal":"European journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 — functional dissection with multiple controls ruling out indirect mechanisms, single lab","pmids":["8566008"],"is_preprint":false},{"year":2003,"finding":"CD154 (CD40L) mRNA stability is regulated by a novel cis-acting instability element in a polypyrimidine-rich region of the 3'UTR; polypyrimidine tract-binding protein (PTB) family members bind this element, with PTB-T decreasing and PTB stabilizing CD154 3'UTR-dependent expression, identifying a post-transcriptional pathway controlling CD40L levels.","method":"RNA-protein pulldown/purification, mass spectrometry identification, reporter gene with tet-inducible system, cotransfection of PTB isoforms","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical purification of binding proteins plus functional reporter assays, single lab","pmids":["12509450"],"is_preprint":false},{"year":2007,"finding":"CD40L interacts directly with integrin Mac-1 (independently of CD40) via flow cytometry, radioactive binding assays, and immunoprecipitation, mediating Mac-1-dependent adhesion, migration, and myeloperoxidase release by inflammatory cells; CD40-deficient mice showed no reduction in atherosclerosis, whereas Mac-1 inhibition attenuated lesion development.","method":"Flow cytometry, radioactive binding assay, immunoprecipitation, in vitro adhesion/migration assays, CD40-KO and Mac-1 inhibition in LDL-receptor-KO mice","journal":"Circulation","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal binding assays plus in vivo genetic/pharmacological validation","pmids":["17372166"],"is_preprint":false},{"year":2006,"finding":"Soluble CD40L (sCD40L) binds to α5β1 integrin on monocytic cells independently of CD40 and αIIbβ3; direct binding of sCD40L to purified α5β1 was confirmed by solid-phase binding assay; sCD40L binding triggers translocation of α5β1 to detergent-insoluble fraction, rapid ERK1/2 MAPK activation, and IL-8 gene expression.","method":"Solid-phase binding assay with purified α5β1, antibody inhibition, ERK1/2 phosphorylation assay, IL-8 gene expression","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — direct binding to purified protein plus signaling readout, identifies novel CD40L receptor","pmids":["17182621"],"is_preprint":false},{"year":2008,"finding":"The CD40–TRAF6 signaling axis is the key regulator of neointima formation and vascular remodeling; CD40 KO mice showed reduced neointima formation with decreased inflammatory cell infiltration and matrix protease activity; mice carrying CD40 transgenes with mutations at TRAF6 binding sites (but not TRAF2/3/5 binding sites) phenocopied CD40 KO, identifying CD40-TRAF6 as the critical downstream pathway.","method":"CD40-/- mouse model, bone marrow reconstitution, transgenic mice with site-specific TRAF-binding mutations, carotid ligation model, intravital microscopy","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with multiple transgenic lines carrying site-specific mutations","pmids":["18195092"],"is_preprint":false},{"year":2014,"finding":"NEDD4 (an E3 ubiquitin ligase) constitutively interacts with CD40 and mediates K63-linked ubiquitination of TRAF3, which is required for CD40-mediated AKT kinase activation; NEDD4 also regulates immunoglobulin class switch by controlling activation-induced cytidine deaminase expression downstream of CD40.","method":"Co-immunoprecipitation, ubiquitination assay (K63-linkage specificity), AKT activation assay, class switch analysis","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus ubiquitination assay with functional AKT readout, single lab","pmids":["25072696"],"is_preprint":false},{"year":2015,"finding":"Small molecules that block CD40–TRAF6 protein-protein interactions (identified by in silico docking and in vitro validation) reduce inflammation in peritonitis and sepsis mouse models without observed systemic side effects, validating the CD40-TRAF6 interface as a druggable target.","method":"In silico docking, in vitro binding assay, mouse models of peritonitis and sepsis","journal":"Journal of chemical information and modeling","confidence":"Medium","confidence_rationale":"Tier 2 — structure-based design validated in vitro and in vivo, single lab","pmids":["25622654"],"is_preprint":false},{"year":2016,"finding":"miR-145 inhibits vascular smooth muscle cell (VSMC) proliferation by directly targeting CD40; overexpression of miR-145 significantly inhibited CD40 expression and VSMC differentiation/proliferation induced by TNF-α, TGF-β, and homocysteine, and decreased IL-6 levels in VSMC supernatants.","method":"miR-145 overexpression, siRNA-mediated CD40 knockdown, proliferation assays, IL-6 ELISA","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 3 — functional KD with phenotypic readout but no direct binding validation of miR-145/CD40 interaction shown","pmids":["27731400"],"is_preprint":false},{"year":2019,"finding":"Staphylococcal superantigens (TSST-1, SEB, SEC) stimulate chemokine (IL-8, MIP-3α) production from human vaginal epithelial cells through CD40; CRISPR-Cas9 knockout of CD40 abolished this response, establishing CD40 as the receptor mediating superantigen-induced mucosal barrier disruption.","method":"CRISPR-Cas9 CD40 knockout, chemokine ELISA, superantigen stimulation assays","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 — CRISPR KO with defined functional readout, single lab","pmids":["30890614"],"is_preprint":false},{"year":2022,"finding":"CD40 signaling in classical type 1 dendritic cells (cDC1s) induces Bcl2l1 (Bcl-xL) expression, which sustains cDC1 survival (by maintaining mitochondrial transmembrane potential and suppressing caspase activation) during anti-tumor CD8 T-cell priming; cDC1-specific CD40 KO reduced migratory cDC1 numbers in tumor-draining lymph nodes, and this was reversed by Bcl2l1 re-expression.","method":"cDC1-specific Cre-driven CD40 KO, mitochondrial potential measurement, caspase activation assay, Bcl2l1 reconstitution, in vitro antigen presentation assay","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 — conditional KO with mechanistic rescue (Bcl2l1 reconstitution) and multiple orthogonal readouts","pmids":["36271147"],"is_preprint":false},{"year":1999,"finding":"CD40 stimulation inhibits Fas- and TNF-receptor-mediated apoptosis in hepatocellular carcinoma cells in a dose-dependent manner by blocking activation of CPP32 (caspase-3).","method":"Anti-CD40 antibody stimulation, apoptosis assays, Western blot for CPP32 activation","journal":"Hepatology","confidence":"Medium","confidence_rationale":"Tier 2 — functional assay with defined molecular mechanism (caspase-3 blockade), single lab","pmids":["10498643"],"is_preprint":false},{"year":1998,"finding":"CD40 associates with JAK3 kinase; however, studies of JAK3-deficient patients show that JAK3 is not essential for CD40-mediated B-cell proliferation, IgE isotype switching, or upregulation of CD23, ICAM-1, CD80, and LT-α.","method":"B-cell stimulation assays in JAK3-deficient patient samples versus normal controls","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 — natural human KO experiment with defined molecular readouts, single lab","pmids":["9746783"],"is_preprint":false}],"current_model":"CD40 is a TNF receptor superfamily member (277 aa, ~50 kDa glycoprotein) that lacks intrinsic kinase activity but signals through its cytoplasmic tail by recruiting TRAF adaptor proteins (TRAF2/3/5 at residues 246–269 and TRAF6 at residues 230–245), which activate NF-κB, JNK/SAPK, and AKT pathways; receptor trimerization (driven by trimeric CD40L) is the minimal signaling unit, forming complexes that also include c-IAP1 and RIP2; downstream, NEDD4-mediated K63-ubiquitination of TRAF3 is required for AKT activation, Act1 negatively regulates signaling, and the TRAF6 axis specifically governs vascular inflammatory responses; beyond its canonical CD40L receptor, CD40L also signals through Mac-1 and α5β1 integrin; in dendritic cells CD40 induces Bcl2l1 to sustain survival during antigen presentation, and alternative splicing of CD40 pre-mRNA generates non-signaling isoforms that limit cellular responsiveness to CD40L."},"narrative":{"teleology":[{"year":1986,"claim":"Identification of CD40 (Bp50) as a B-cell surface molecule that delivers costimulatory activation signals established the gene's foundational role in B-cell biology, distinguishing it from surface immunoglobulin.","evidence":"Monoclonal antibody stimulation of purified tonsillar B cells with cell-cycle analysis","pmids":["3487090"],"confidence":"High","gaps":["Molecular identity and sequence unknown","Signaling mechanism uncharacterized","Expression on non-B cells not investigated"]},{"year":1989,"claim":"Molecular cloning of CD40 revealed homology to the nerve growth factor receptor, placing it in what became the TNF receptor superfamily and predicting a cytoplasmic signaling tail without intrinsic kinase activity.","evidence":"cDNA cloning and sequence analysis with transition matrix homology method","pmids":["2475341"],"confidence":"High","gaps":["Ligand not yet identified","Downstream signaling adaptors unknown","Function of cytoplasmic tail not tested"]},{"year":1994,"claim":"Functional studies established that CD40–CD40L interactions drive immunoglobulin class switching, germinal center formation, and memory B-cell generation in vivo, and that CD40L deficiency causes X-linked hyper-IgM syndrome, defining CD40 as essential for humoral immunity.","evidence":"In vivo anti-CD40L antibody blockade in mice, adoptive transfer, B-cell culture with recombinant CD40L and cytokines, human genetics","pmids":["7516669","7516405"],"confidence":"High","gaps":["Intracellular signal transduction pathway unresolved","Role in non-lymphoid tissues unclear"]},{"year":1995,"claim":"Discovery that TRAF2 directly binds the CD40 cytoplasmic tail and mediates NF-κB activation identified the first signal-transduction mechanism downstream of CD40, explaining how a receptor without intrinsic kinase activity signals.","evidence":"Yeast two-hybrid, dominant-negative TRAF2 overexpression blocking CD40-induced CD23 and NF-κB reporter activation","pmids":["7533327","7544915"],"confidence":"High","gaps":["Binding sites for other TRAF family members not mapped","In vivo relevance of individual TRAFs untested"]},{"year":1995,"claim":"Demonstration that CD40 is expressed and functional on vascular endothelial cells—where ligation induces E-selectin, VCAM-1, and ICAM-1—extended CD40 biology beyond the immune system into vascular inflammation.","evidence":"Flow cytometry, recombinant CD40L stimulation, adhesion assays on human endothelial cells","pmids":["7540655","7538666"],"confidence":"High","gaps":["Relative contribution of TRAF pathways in endothelial vs. immune cells unknown","In vivo vascular consequences not yet tested"]},{"year":1996,"claim":"Mapping of TRAF6 to a distinct cytoplasmic domain region (residues 230–245, separate from TRAF2/3/5 at 246–269) revealed that CD40 engages two parallel TRAF signaling axes, each activating NF-κB through different mechanisms.","evidence":"Yeast two-hybrid deletion analysis and NF-κB reporter assays","pmids":["8910514"],"confidence":"High","gaps":["Functional distinction of TRAF6 vs. TRAF2/3/5 pathways in vivo not delineated","Structural basis of TRAF6 recognition unknown"]},{"year":1996,"claim":"CD40 signaling on antigen-presenting cells was shown to upregulate B7 costimulatory molecules, providing the mechanistic link by which CD40L-expressing T helper cells license dendritic cells and macrophages for T-cell priming.","evidence":"CD40L-deficient mouse reconstitution with agonistic anti-CD40 antibody, anti-B7 blockade","pmids":["8791591"],"confidence":"High","gaps":["Downstream survival signals in DCs not characterized","Relative contribution of CD80 vs. CD86 unclear"]},{"year":1998,"claim":"In vivo antibody blockade of CD40L dramatically reduced atherosclerotic lesion formation in hyperlipidemic mice, establishing a causal role for the CD40–CD40L axis in atherogenesis beyond its immune functions.","evidence":"Anti-CD40L treatment in LDL-receptor KO mice on high-cholesterol diet with morphometry and immunohistochemistry","pmids":["9671306"],"confidence":"High","gaps":["Whether CD40 on immune cells or vascular cells drives atherogenesis not resolved","Relative contribution of TRAF6 vs. TRAF2/3/5 in atherogenesis untested"]},{"year":1999,"claim":"The crystal structure of the TRAF2–CD40 peptide complex at 2.4 Å revealed the trimeric mushroom-shaped TRAF2 architecture and showed that each TRAF monomer rim binds one CD40 peptide in an extended conformation, providing the structural basis for ligand-induced receptor trimerization as the minimal signaling unit.","evidence":"X-ray crystallography at 2.4 Å resolution","pmids":["10411888"],"confidence":"High","gaps":["Full-length receptor–TRAF complex structure unavailable","Dynamics of signalosome assembly not captured"]},{"year":2001,"claim":"Reconstitution experiments with soluble trimeric CD40 cytoplasmic domains showed that trimerization is sufficient for NF-κB activation and that the signaling complex contains TRAF2, TRAF3, TRAF5, TRAF6, and c-IAP1, defining the complete core signalosome composition.","evidence":"Myristoylated multimeric CD40 cytoplasmic domain constructs, immunoprecipitation, NF-κB reporter assay","pmids":["11562359"],"confidence":"High","gaps":["Stoichiometry of TRAF molecules per CD40 trimer unknown","Post-translational modifications of TRAFs in the complex not characterized"]},{"year":2001,"claim":"Alternative splicing of CD40 pre-mRNA was found to generate non-signaling isoforms that accumulate during macrophage/DC activation, revealing a cell-intrinsic negative feedback mechanism that limits CD40 responsiveness over time.","evidence":"RT-PCR and IL-12 p40 reporter assay in macrophages and DCs transfected with individual isoforms","pmids":["11172023"],"confidence":"Medium","gaps":["Splicing factors controlling the switch not identified","In vivo relevance of isoform ratio not demonstrated","Whether isoforms act as dominant negatives at the cell surface or intracellularly not resolved"]},{"year":2002,"claim":"The TRAF6–CD40 crystal structure revealed a Pro-X-Glu-X-X-(aromatic/acidic) binding motif oriented 40° differently from TRAF2 peptide binding, providing the structural explanation for why TRAF6 engages a distinct CD40 cytoplasmic domain and enabling design of TRAF6-blocking peptides.","evidence":"X-ray crystallography of TRAF6–CD40 peptide complex, cell-permeable peptide inhibition","pmids":["12140561"],"confidence":"High","gaps":["Whether peptide inhibitors are selective in vivo unknown","Cooperativity between TRAF2/3/5 and TRAF6 binding on the same receptor trimer not addressed"]},{"year":2004,"claim":"Genetic epistasis using Act1-KO and Act1/CD40 double-KO mice identified Act1 as a negative regulator of CD40 signaling that restrains NF-κB processing, JNK, ERK, and p38 activation in B cells, establishing a cell-intrinsic brake on CD40 pathway output.","evidence":"Act1-KO and Act1/CD40 double-KO B-cell signaling assays","pmids":["15485634"],"confidence":"High","gaps":["Mechanism by which Act1 inhibits TRAF signaling not defined","Act1 relevance in non-B-cell CD40 contexts untested"]},{"year":2007,"claim":"CD40L was shown to interact directly with integrin Mac-1 independently of CD40, mediating inflammatory cell adhesion and migration; Mac-1 inhibition—but not CD40 deficiency—attenuated atherosclerosis in vivo, revealing that some CD40L-driven vascular inflammation is CD40-independent.","evidence":"Multiple binding assays (flow cytometry, radioactive binding, co-IP) plus CD40-KO and Mac-1 inhibition in LDL-receptor KO mice","pmids":["17372166"],"confidence":"High","gaps":["Relative contribution of Mac-1 vs. α5β1 integrin in CD40L-independent signaling not compared","Whether CD40L simultaneously engages CD40 and integrins on the same cell not tested"]},{"year":2008,"claim":"Transgenic mice carrying CD40 with site-specific TRAF6-binding mutations phenocopied CD40-KO in neointima formation, while TRAF2/3/5-binding mutations did not, establishing the TRAF6 axis as the critical mediator of CD40-driven vascular inflammatory remodeling.","evidence":"TRAF-binding site mutant CD40 transgenic mice, carotid ligation model, bone marrow reconstitution","pmids":["18195092"],"confidence":"High","gaps":["Whether TRAF6 pathway dominance is specific to vascular cells or generalizable not resolved","Downstream effectors of TRAF6 in vascular remodeling not fully mapped"]},{"year":2014,"claim":"NEDD4 was identified as a constitutive CD40-associated E3 ubiquitin ligase that K63-ubiquitinates TRAF3, a modification required for CD40-mediated AKT activation and AID-dependent immunoglobulin class switching, adding a ubiquitin-dependent branch to CD40 signaling.","evidence":"Co-immunoprecipitation, K63-linkage-specific ubiquitination assay, AKT activation and class-switch analysis","pmids":["25072696"],"confidence":"Medium","gaps":["Whether NEDD4 also modifies other CD40-associated TRAFs not tested","Structural basis of NEDD4–CD40 interaction unknown","In vivo confirmation in NEDD4-conditional KO not performed"]},{"year":2022,"claim":"Conditional deletion of CD40 in cDC1s revealed that CD40 sustains dendritic cell survival during anti-tumor T-cell priming by inducing Bcl2l1 (Bcl-xL), which maintains mitochondrial potential and blocks caspase activation—directly linking CD40 signaling to DC longevity in the tumor microenvironment.","evidence":"cDC1-specific Cre-driven CD40 KO, mitochondrial potential and caspase assays, Bcl2l1 reconstitution rescue","pmids":["36271147"],"confidence":"High","gaps":["Whether Bcl2l1 induction operates through TRAF2/3/5 or TRAF6 not determined","Relevance to non-tumor inflammatory DC survival unknown"]},{"year":null,"claim":"Key unresolved questions include: the structural basis of full-length CD40 signalosome assembly beyond peptide-level TRAF interactions; the cell-type-specific logic that determines TRAF6 vs. TRAF2/3/5 pathway dominance; the splicing regulators controlling non-signaling CD40 isoform production; and whether simultaneous CD40L engagement of CD40 and integrins on the same cell creates composite signaling outputs.","evidence":"","pmids":[],"confidence":"Low","gaps":["Full-length receptor–TRAF signalosome structure not solved","Cell-type-specific TRAF pathway selection mechanism unknown","Splicing factors regulating CD40 isoform switching not identified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0,1,3,6,7,19]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[6,19,27]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1,3,8,9]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,4,10,17,38]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6,7,19,25,27,34]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[18,33,36]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[38,39]}],"complexes":[],"partners":["TRAF2","TRAF3","TRAF5","TRAF6","CD40LG","BIRC2","NEDD4","TRAF3IP2"],"other_free_text":[]},"mechanistic_narrative":"CD40 is a TNF receptor superfamily member that functions as a master costimulatory receptor on B cells, dendritic cells, macrophages, and endothelial cells, coupling adaptive immune activation to vascular inflammation and antigen presentation. CD40 lacks intrinsic enzymatic activity and instead signals by recruiting TRAF adaptor proteins to two distinct cytoplasmic tail regions—TRAF2/3/5 bind residues 246–269 and TRAF6 binds residues 230–245—with trimeric receptor assembly as the minimal signaling unit that activates NF-κB, JNK/SAPK, p44/42 MAPK, and AKT pathways [PMID:7533327, PMID:8910514, PMID:11562359, PMID:10411888]. Functionally, CD40 ligation drives B-cell proliferation and immunoglobulin class switching, upregulates B7 costimulatory molecules on antigen-presenting cells to license T-cell priming, sustains dendritic cell survival via Bcl2l1 induction, and activates endothelial cells to express adhesion molecules and angiogenesis factors; the TRAF6 axis specifically governs vascular inflammatory remodeling [PMID:7516669, PMID:8791591, PMID:36271147, PMID:7540655, PMID:18195092]. Deficiency of its ligand CD40L causes X-linked hyper-IgM syndrome, and alternative splicing of CD40 pre-mRNA generates non-signaling isoforms that attenuate cellular responsiveness [PMID:7516669, PMID:11172023]."},"prefetch_data":{"uniprot":{"accession":"P25942","full_name":"Tumor necrosis factor receptor superfamily member 5","aliases":["B-cell surface antigen CD40","Bp50","CD40L receptor","CDw40"],"length_aa":277,"mass_kda":30.6,"function":"Receptor for TNFSF5/CD40LG (PubMed:31331973). Transduces TRAF6- and MAP3K8-mediated signals that activate ERK in macrophages and B cells, leading to induction of immunoglobulin secretion (By similarity)","subcellular_location":"Secreted","url":"https://www.uniprot.org/uniprotkb/P25942/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CD40","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CD40","total_profiled":1310},"omim":[{"mim_id":"619289","title":"ZINC FINGER PROTEIN 91, ATYPICAL E3 UBIQUITIN LIGASE; ZFP91","url":"https://www.omim.org/entry/619289"},{"mim_id":"619238","title":"IMMUNODEFICIENCY 79; IMD79","url":"https://www.omim.org/entry/619238"},{"mim_id":"619158","title":"PHOSPHATIDYLINOSITOL 3-KINASE-INTERACTING PROTEIN 1; PIK3IP1","url":"https://www.omim.org/entry/619158"},{"mim_id":"616005","title":"IMMUNODEFICIENCY 36 WITH LYMPHOPROLIFERATION; IMD36","url":"https://www.omim.org/entry/616005"},{"mim_id":"615772","title":"WAP FOUR-DISULFIDE CORE DOMAIN 21, PSEUDOGENE; WFDC21P","url":"https://www.omim.org/entry/615772"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"lymphoid tissue","ntpm":52.9}],"url":"https://www.proteinatlas.org/search/CD40"},"hgnc":{"alias_symbol":["p50","Bp50"],"prev_symbol":["TNFRSF5"]},"alphafold":{"accession":"P25942","domains":[{"cath_id":"2.10.50.10","chopping":"29-78","consensus_level":"medium","plddt":96.321,"start":29,"end":78},{"cath_id":"2.10.50.10","chopping":"122-213","consensus_level":"medium","plddt":92.5813,"start":122,"end":213}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P25942","model_url":"https://alphafold.ebi.ac.uk/files/AF-P25942-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P25942-F1-predicted_aligned_error_v6.png","plddt_mean":81.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CD40","jax_strain_url":"https://www.jax.org/strain/search?query=CD40"},"sequence":{"accession":"P25942","fasta_url":"https://rest.uniprot.org/uniprotkb/P25942.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P25942/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P25942"}},"corpus_meta":[{"pmid":"9597126","id":"PMC_9597126","title":"CD40 and CD154 in cell-mediated immunity.","date":"1998","source":"Annual review of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/9597126","citation_count":1165,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10647992","id":"PMC_10647992","title":"CD40-CD40 ligand.","date":"2000","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/10647992","citation_count":1127,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"7516669","id":"PMC_7516669","title":"The CD40 antigen and its ligand.","date":"1994","source":"Annual review of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/7516669","citation_count":1092,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8717526","id":"PMC_8717526","title":"Immune regulation by CD40 and its ligand GP39.","date":"1996","source":"Annual review of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/8717526","citation_count":504,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"3487090","id":"PMC_3487090","title":"Activation of human B cells mediated through two distinct cell surface differentiation antigens, Bp35 and Bp50.","date":"1986","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/3487090","citation_count":496,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11739273","id":"PMC_11739273","title":"CD40 signaling and plaque instability.","date":"2001","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/11739273","citation_count":483,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"7533327","id":"PMC_7533327","title":"Involvement of CRAF1, a relative of TRAF, in CD40 signaling.","date":"1995","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/7533327","citation_count":439,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31412220","id":"PMC_31412220","title":"CD40 Agonist Antibodies in Cancer Immunotherapy.","date":"2019","source":"Annual review of medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31412220","citation_count":431,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8637903","id":"PMC_8637903","title":"CD40-CD40 ligand interactions in experimental allergic encephalomyelitis and multiple sclerosis.","date":"1996","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/8637903","citation_count":409,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"7540655","id":"PMC_7540655","title":"Expression of functional CD40 by vascular endothelial cells.","date":"1995","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/7540655","citation_count":360,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23460534","id":"PMC_23460534","title":"Agonistic CD40 antibodies and cancer therapy.","date":"2013","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/23460534","citation_count":356,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8791591","id":"PMC_8791591","title":"CD40 ligand-dependent T cell activation: requirement of B7-CD28 signaling through CD40.","date":"1996","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8791591","citation_count":320,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19679244","id":"PMC_19679244","title":"The CD40/CD40 ligand system: linking inflammation with atherothrombosis.","date":"2009","source":"Journal of the American College of Cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/19679244","citation_count":301,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8408024","id":"PMC_8408024","title":"Raf exists in a native heterocomplex with hsp90 and p50 that can be reconstituted in a cell-free system.","date":"1993","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8408024","citation_count":277,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9529257","id":"PMC_9529257","title":"Cotranslational biogenesis of NF-kappaB p50 by the 26S proteasome.","date":"1998","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/9529257","citation_count":273,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9182676","id":"PMC_9182676","title":"A new mechanism of NK cell cytotoxicity activation: the CD40-CD40 ligand interaction.","date":"1997","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/9182676","citation_count":190,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11705814","id":"PMC_11705814","title":"Upregulation of CD40 and CD40 ligand (CD154) in patients with moderate hypercholesterolemia.","date":"2001","source":"Circulation","url":"https://pubmed.ncbi.nlm.nih.gov/11705814","citation_count":184,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17372166","id":"PMC_17372166","title":"CD40 ligand mediates inflammation independently of CD40 by interaction with Mac-1.","date":"2007","source":"Circulation","url":"https://pubmed.ncbi.nlm.nih.gov/17372166","citation_count":180,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10411888","id":"PMC_10411888","title":"Crystallographic analysis of CD40 recognition and signaling by human TRAF2.","date":"1999","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/10411888","citation_count":166,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16826459","id":"PMC_16826459","title":"Heritability and reliability of P300, P50 and duration mismatch negativity.","date":"2006","source":"Behavior genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16826459","citation_count":155,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10449775","id":"PMC_10449775","title":"Targeted disruption of Traf5 gene causes defects in CD40- and CD27-mediated lymphocyte activation.","date":"1999","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/10449775","citation_count":152,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17317815","id":"PMC_17317815","title":"Prospect of targeting the CD40 pathway for cancer therapy.","date":"2007","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/17317815","citation_count":149,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17633023","id":"PMC_17633023","title":"TRAF proteins in CD40 signaling.","date":"2007","source":"Advances in experimental medicine and biology","url":"https://pubmed.ncbi.nlm.nih.gov/17633023","citation_count":146,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8809473","id":"PMC_8809473","title":"Functions of CD40 and its ligand, gp39 (CD40L).","date":"1996","source":"Critical reviews in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/8809473","citation_count":139,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12764232","id":"PMC_12764232","title":"Upregulation of CD40-CD40 ligand (CD154) in patients with acute cerebral ischemia.","date":"2003","source":"Stroke","url":"https://pubmed.ncbi.nlm.nih.gov/12764232","citation_count":134,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20579762","id":"PMC_20579762","title":"The NF-kappaB p50:p50:HDAC-1 repressor complex orchestrates transcriptional inhibition of multiple pro-inflammatory genes.","date":"2010","source":"Journal of hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/20579762","citation_count":133,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"7907604","id":"PMC_7907604","title":"Cyclosporin A inhibits CD40 ligand expression in T lymphocytes.","date":"1994","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/7907604","citation_count":132,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9368772","id":"PMC_9368772","title":"The CD40 pathway in allograft rejection, acceptance, and tolerance.","date":"1997","source":"Current opinion in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/9368772","citation_count":125,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8647193","id":"PMC_8647193","title":"Human dendritic cells activate T lymphocytes via a CD40: CD40 ligand-dependent pathway.","date":"1996","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/8647193","citation_count":122,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"18977174","id":"PMC_18977174","title":"CD40-CD40 ligand interactions in oxidative stress, inflammation and vascular disease.","date":"2008","source":"Trends in molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/18977174","citation_count":119,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11172023","id":"PMC_11172023","title":"Regulation of CD40 function by its isoforms generated through alternative splicing.","date":"2001","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/11172023","citation_count":118,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15485634","id":"PMC_15485634","title":"Act1, a negative regulator in CD40- and BAFF-mediated B cell survival.","date":"2004","source":"Immunity","url":"https://pubmed.ncbi.nlm.nih.gov/15485634","citation_count":114,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12906261","id":"PMC_12906261","title":"CD40 and dendritic cell function.","date":"2003","source":"Critical reviews in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/12906261","citation_count":113,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19652870","id":"PMC_19652870","title":"The multi-functionality of CD40L and its receptor CD40 in atherosclerosis.","date":"2009","source":"Thrombosis and haemostasis","url":"https://pubmed.ncbi.nlm.nih.gov/19652870","citation_count":113,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25331559","id":"PMC_25331559","title":"Redox regulation of NF-κB p50 and M1 polarization in microglia.","date":"2014","source":"Glia","url":"https://pubmed.ncbi.nlm.nih.gov/25331559","citation_count":112,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10741409","id":"PMC_10741409","title":"Chemokines and CD40 expression in human fibroblasts.","date":"2000","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/10741409","citation_count":104,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11567031","id":"PMC_11567031","title":"NF-kappaB1 (p50) homodimers contribute to transcription of the bcl-2 oncogene.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11567031","citation_count":103,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11847112","id":"PMC_11847112","title":"CD40 is expressed and functional on neuronal cells.","date":"2002","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/11847112","citation_count":101,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17482093","id":"PMC_17482093","title":"CD40 and its ligand in atherosclerosis.","date":"2007","source":"Trends in cardiovascular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/17482093","citation_count":101,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19519322","id":"PMC_19519322","title":"The biological functions of NF-kappaB1 (p50) and its potential as an anti-cancer target.","date":"2009","source":"Current cancer drug targets","url":"https://pubmed.ncbi.nlm.nih.gov/19519322","citation_count":100,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"1696597","id":"PMC_1696597","title":"Association between IL-6 and CD40 signaling. IL-6 induces phosphorylation of CD40 receptors.","date":"1990","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/1696597","citation_count":100,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15078798","id":"PMC_15078798","title":"Upregulation of the CD40/CD40 ligand dyad and platelet-monocyte aggregation in cigarette smokers.","date":"2004","source":"Circulation","url":"https://pubmed.ncbi.nlm.nih.gov/15078798","citation_count":96,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29773027","id":"PMC_29773027","title":"Functions of CD40 and Its Ligand, gp39 (CD40L).","date":"2017","source":"Critical reviews in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29773027","citation_count":90,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27427981","id":"PMC_27427981","title":"p21 mediates macrophage reprogramming through regulation of p50-p50 NF-κB and IFN-β.","date":"2016","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/27427981","citation_count":89,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9250584","id":"PMC_9250584","title":"Functional role of CD40 and its ligand.","date":"1997","source":"International archives of allergy and immunology","url":"https://pubmed.ncbi.nlm.nih.gov/9250584","citation_count":85,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17182621","id":"PMC_17182621","title":"CD40 ligand binds to alpha5beta1 integrin and triggers cell signaling.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17182621","citation_count":85,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"3500063","id":"PMC_3500063","title":"Synergistic interaction between interleukin 4 and anti-Bp50 (CDw40) revealed in a novel B cell restimulation assay.","date":"1987","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/3500063","citation_count":84,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"33804039","id":"PMC_33804039","title":"Agonistic CD40 Antibodies in Cancer Treatment.","date":"2021","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/33804039","citation_count":83,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"18195092","id":"PMC_18195092","title":"The CD40-TRAF6 axis is the key regulator of the CD40/CD40L system in neointima formation and arterial remodeling.","date":"2008","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/18195092","citation_count":79,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11268217","id":"PMC_11268217","title":"Regulation of CD40 and CD40 ligand by the AT-hook transcription factor AKNA.","date":"2001","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/11268217","citation_count":73,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"14668329","id":"PMC_14668329","title":"Bcl-3 and NFkappaB p50-p50 homodimers act as transcriptional repressors in tolerant CD4+ T cells.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/14668329","citation_count":73,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12509450","id":"PMC_12509450","title":"Delineation of a novel pathway that regulates CD154 (CD40 ligand) expression.","date":"2003","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/12509450","citation_count":71,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15543947","id":"PMC_15543947","title":"The p50-p50 NF-kappaB complex as a stimulus-specific repressor of gene activation.","date":"2004","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15543947","citation_count":69,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11162447","id":"PMC_11162447","title":"Identification of mouse YB1/p50 as a component of the FMRP-associated mRNP particle.","date":"2000","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/11162447","citation_count":69,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21928689","id":"PMC_21928689","title":"CD40/CD40 ligand interactions in immune responses and pulmonary immunity.","date":"2011","source":"Nagoya journal of medical science","url":"https://pubmed.ncbi.nlm.nih.gov/21928689","citation_count":68,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"2965643","id":"PMC_2965643","title":"Soluble CD23 is released by B lymphocytes cycling in response to interleukin 4 and anti-Bp50 (CDw40).","date":"1988","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/2965643","citation_count":68,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11163401","id":"PMC_11163401","title":"Role for CD40-CD40 ligand interactions in the immune response to solid tumours.","date":"2000","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/11163401","citation_count":67,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17154264","id":"PMC_17154264","title":"TACI attenuates antibody production costimulated by BAFF-R and CD40.","date":"2007","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/17154264","citation_count":65,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9837692","id":"PMC_9837692","title":"Blockade of CD40-CD40 ligand interactions protects against radiation-induced pulmonary inflammation and fibrosis.","date":"1998","source":"Clinical immunology and immunopathology","url":"https://pubmed.ncbi.nlm.nih.gov/9837692","citation_count":65,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23788426","id":"PMC_23788426","title":"Resolvin D1 stimulates efferocytosis through p50/p50-mediated suppression of tumor necrosis factor-α expression.","date":"2013","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/23788426","citation_count":65,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9144474","id":"PMC_9144474","title":"Bidirectional regulation of human B cell responses by CD40-CD40 ligand interactions.","date":"1997","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/9144474","citation_count":63,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12874247","id":"PMC_12874247","title":"Proangiogenic function of CD40 ligand-CD40 interactions.","date":"2003","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/12874247","citation_count":61,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"7507684","id":"PMC_7507684","title":"Role of CD40-CD40-ligand interaction in Ig-isotype switching.","date":"1993","source":"Current opinion in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/7507684","citation_count":57,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"7564113","id":"PMC_7564113","title":"Inhibition of the CD40-CD40ligand pathway prevents murine membranous glomerulonephritis.","date":"1995","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/7564113","citation_count":57,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25622654","id":"PMC_25622654","title":"Discovery of small molecule CD40-TRAF6 inhibitors.","date":"2015","source":"Journal of chemical information and modeling","url":"https://pubmed.ncbi.nlm.nih.gov/25622654","citation_count":56,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31403344","id":"PMC_31403344","title":"Concepts for agonistic targeting of CD40 in immuno-oncology.","date":"2019","source":"Human vaccines & immunotherapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/31403344","citation_count":55,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25681350","id":"PMC_25681350","title":"RelB/p50 complexes regulate cytokine-induced YKL-40 expression.","date":"2015","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/25681350","citation_count":55,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11986322","id":"PMC_11986322","title":"Role of p50/CDC37 in hepadnavirus assembly and replication.","date":"2002","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11986322","citation_count":53,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12181450","id":"PMC_12181450","title":"2,3,7,8-Tetrachlorodibenzo-p-dioxin suppresses tumor necrosis factor-alpha and anti-CD40-induced activation of NF-kappaB/Rel in dendritic cells: p50 homodimer activation is not affected.","date":"2002","source":"Molecular pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/12181450","citation_count":53,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"36271147","id":"PMC_36271147","title":"Mechanisms of CD40-dependent cDC1 licensing beyond costimulation.","date":"2022","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/36271147","citation_count":52,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26268734","id":"PMC_26268734","title":"Update on CD40 and CD154 blockade in transplant models.","date":"2015","source":"Immunotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/26268734","citation_count":52,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19647448","id":"PMC_19647448","title":"The Janus faces of CD40 in cancer.","date":"2009","source":"Seminars in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/19647448","citation_count":52,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26497740","id":"PMC_26497740","title":"The NF-κB p65 and p50 homodimer cooperate with IRF8 to activate iNOS transcription.","date":"2015","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/26497740","citation_count":52,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10985254","id":"PMC_10985254","title":"The emerging role of CD40 ligand in HIV infection.","date":"2000","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/10985254","citation_count":51,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12969144","id":"PMC_12969144","title":"Blockade of CD40-CD40 ligand protects against renal injury in chronic proteinuric renal disease.","date":"2003","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/12969144","citation_count":51,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11283856","id":"PMC_11283856","title":"Normal liver regeneration in p50/nuclear factor kappaB1 knockout mice.","date":"2001","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/11283856","citation_count":50,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17324402","id":"PMC_17324402","title":"CD40-CD40 ligand mediates the recruitment of leukocytes and platelets in the inflamed murine colon.","date":"2006","source":"Gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/17324402","citation_count":49,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35456932","id":"PMC_35456932","title":"CD40-CD40L in Neurological Disease.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35456932","citation_count":49,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27731400","id":"PMC_27731400","title":"miRNA-145 inhibits VSMC proliferation by targeting CD40.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27731400","citation_count":49,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31660072","id":"PMC_31660072","title":"CapG promotes resistance to paclitaxel in breast cancer through transactivation of PIK3R1/P50.","date":"2019","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/31660072","citation_count":48,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10498643","id":"PMC_10498643","title":"Expression of functional CD40 in human hepatocellular carcinoma.","date":"1999","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/10498643","citation_count":47,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15367912","id":"PMC_15367912","title":"CD40 ligand gene and Kawasaki disease.","date":"2004","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/15367912","citation_count":46,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10569134","id":"PMC_10569134","title":"CD30/CD30 ligand and CD40/CD40 ligand in malignant lymphoid disorders.","date":"1999","source":"The International journal of biological markers","url":"https://pubmed.ncbi.nlm.nih.gov/10569134","citation_count":45,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25072696","id":"PMC_25072696","title":"NEDD4 ubiquitinates TRAF3 to promote CD40-mediated AKT activation.","date":"2014","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/25072696","citation_count":45,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23396362","id":"PMC_23396362","title":"NF-κB1 p50 promotes p53 protein translation through miR-190 downregulation of PHLPP1.","date":"2013","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/23396362","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12510151","id":"PMC_12510151","title":"Differential regulation of cell survival by CD40.","date":"2003","source":"Apoptosis : an international journal on programmed cell death","url":"https://pubmed.ncbi.nlm.nih.gov/12510151","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20382965","id":"PMC_20382965","title":"Targeted deletion of NF-kappaB p50 diminishes the cardioprotection of histone deacetylase inhibition.","date":"2010","source":"American journal of physiology. Heart and circulatory physiology","url":"https://pubmed.ncbi.nlm.nih.gov/20382965","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11056083","id":"PMC_11056083","title":"Immune regulation by CD40-CD40-l interactions - 2; Y2K update.","date":"2000","source":"Frontiers in bioscience : a journal and virtual library","url":"https://pubmed.ncbi.nlm.nih.gov/11056083","citation_count":42,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"18287517","id":"PMC_18287517","title":"A functional TNFRSF5 gene variant is associated with risk of lymphoma.","date":"2008","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/18287517","citation_count":41,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11562359","id":"PMC_11562359","title":"Molecular characterization of CD40 signaling intermediates.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11562359","citation_count":41,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11042507","id":"PMC_11042507","title":"CD40 ligand in CLL pathogenesis and therapy.","date":"2000","source":"Leukemia & lymphoma","url":"https://pubmed.ncbi.nlm.nih.gov/11042507","citation_count":39,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8566008","id":"PMC_8566008","title":"CD40-CD40 ligand interactions stimulate B cell antigen processing.","date":"1995","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/8566008","citation_count":37,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17823201","id":"PMC_17823201","title":"Blockade of CD40/CD40 ligand interactions attenuates skin fibrosis and autoimmunity in the tight-skin mouse.","date":"2007","source":"Annals of the rheumatic diseases","url":"https://pubmed.ncbi.nlm.nih.gov/17823201","citation_count":37,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26474561","id":"PMC_26474561","title":"The association of CD40 polymorphisms with CD40 serum levels and risk of systemic lupus erythematosus.","date":"2015","source":"BMC genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26474561","citation_count":34,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30890614","id":"PMC_30890614","title":"Staphylococcal Superantigens Stimulate Epithelial Cells through CD40 To Produce Chemokines.","date":"2019","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/30890614","citation_count":34,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9086433","id":"PMC_9086433","title":"CD40/CD40 ligand interactions in normal, reactive and malignant lympho-hematopoietic tissues.","date":"1997","source":"Leukemia & lymphoma","url":"https://pubmed.ncbi.nlm.nih.gov/9086433","citation_count":33,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19175598","id":"PMC_19175598","title":"Inhibition of allergic responses by CD40 gene silencing.","date":"2009","source":"Allergy","url":"https://pubmed.ncbi.nlm.nih.gov/19175598","citation_count":33,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17917059","id":"PMC_17917059","title":"Roles of TRAF6 in CD40 signaling.","date":"2007","source":"Immunologic research","url":"https://pubmed.ncbi.nlm.nih.gov/17917059","citation_count":32,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"1708162","id":"PMC_1708162","title":"Expression of CD40 and CD43 during activation of human B lymphocytes.","date":"1991","source":"Scandinavian journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/1708162","citation_count":31,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9746783","id":"PMC_9746783","title":"Role of JAK3 in CD40-mediated signaling.","date":"1998","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/9746783","citation_count":31,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23128233","id":"PMC_23128233","title":"Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.","date":"2012","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/23128233","citation_count":3725,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21833088","id":"PMC_21833088","title":"Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.","date":"2011","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/21833088","citation_count":2101,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"24390342","id":"PMC_24390342","title":"Genetics of rheumatoid arthritis contributes to biology and drug discovery.","date":"2013","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/24390342","citation_count":1778,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"9468137","id":"PMC_9468137","title":"CD40 ligand on activated platelets triggers an inflammatory reaction of endothelial cells.","date":"1998","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/9468137","citation_count":1646,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"9624004","id":"PMC_9624004","title":"Help for cytotoxic-T-cell responses is mediated by CD40 signalling.","date":"1998","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/9624004","citation_count":1537,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12477932","id":"PMC_12477932","title":"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.","date":"2002","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12477932","citation_count":1479,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"9020361","id":"PMC_9020361","title":"MAP3K-related kinase involved in NF-kappaB induction by TNF, CD95 and IL-1.","date":"1997","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/9020361","citation_count":1121,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"9384571","id":"PMC_9384571","title":"The c-IAP-1 and c-IAP-2 proteins are direct inhibitors of specific caspases.","date":"1997","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9384571","citation_count":1060,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"20453842","id":"PMC_20453842","title":"Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.","date":"2010","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20453842","citation_count":1018,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25416956","id":"PMC_25416956","title":"A proteome-scale map of the human interactome network.","date":"2014","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/25416956","citation_count":977,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"7544915","id":"PMC_7544915","title":"TRAF2-mediated activation of NF-kappa B by TNF receptor 2 and CD40.","date":"1995","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/7544915","citation_count":938,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"7859281","id":"PMC_7859281","title":"The Epstein-Barr virus transforming protein LMP1 engages signaling proteins for the tumor necrosis factor receptor family.","date":"1995","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/7859281","citation_count":885,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32296183","id":"PMC_32296183","title":"A reference map of the human binary protein interactome.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32296183","citation_count":849,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"9671306","id":"PMC_9671306","title":"Reduction of atherosclerosis in mice by inhibition of CD40 signalling.","date":"1998","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/9671306","citation_count":735,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"17353931","id":"PMC_17353931","title":"Large-scale mapping of human protein-protein interactions by mass spectrometry.","date":"2007","source":"Molecular systems biology","url":"https://pubmed.ncbi.nlm.nih.gov/17353931","citation_count":733,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"33961781","id":"PMC_33961781","title":"Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.","date":"2021","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/33961781","citation_count":705,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21873635","id":"PMC_21873635","title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.","date":"2011","source":"Briefings in bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/21873635","citation_count":656,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"2475341","id":"PMC_2475341","title":"A B-lymphocyte activation molecule related to the nerve growth factor receptor and induced by cytokines in carcinomas.","date":"1989","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/2475341","citation_count":594,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"9050882","id":"PMC_9050882","title":"Functional CD40 ligand is expressed on human vascular endothelial cells, smooth muscle cells, and macrophages: implications for CD40-CD40 ligand signaling in atherosclerosis.","date":"1997","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/9050882","citation_count":592,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12140561","id":"PMC_12140561","title":"Distinct molecular mechanism for initiating TRAF6 signalling.","date":"2002","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/12140561","citation_count":542,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"8125298","id":"PMC_8125298","title":"Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides.","date":"1994","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/8125298","citation_count":492,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25910212","id":"PMC_25910212","title":"Widespread macromolecular interaction perturbations in human genetic disorders.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/25910212","citation_count":454,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"18794853","id":"PMC_18794853","title":"Common variants at CD40 and other loci confer risk of rheumatoid arthritis.","date":"2008","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18794853","citation_count":445,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"15489334","id":"PMC_15489334","title":"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).","date":"2004","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/15489334","citation_count":438,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"19525955","id":"PMC_19525955","title":"Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20.","date":"2009","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19525955","citation_count":433,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26871637","id":"PMC_26871637","title":"Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.","date":"2016","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26871637","citation_count":423,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"8910514","id":"PMC_8910514","title":"Identification of TRAF6, a novel tumor necrosis factor receptor-associated factor protein that mediates signaling from an amino-terminal domain of the CD40 cytoplasmic region.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8910514","citation_count":418,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"7538666","id":"PMC_7538666","title":"CD40 on human endothelial cells: inducibility by cytokines and functional regulation of adhesion molecule expression.","date":"1995","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/7538666","citation_count":411,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"9642260","id":"PMC_9642260","title":"RIP2 is a novel NF-kappaB-activating and cell death-inducing kinase.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9642260","citation_count":383,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"7516405","id":"PMC_7516405","title":"gp39-CD40 interactions are essential for germinal center formation and the development of B cell memory.","date":"1994","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/7516405","citation_count":368,"is_preprint":false,"source_track":"gene2pubmed"}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":44761,"output_tokens":5451,"usd":0.108024},"stage2":{"model":"claude-opus-4-6","input_tokens":9063,"output_tokens":3349,"usd":0.19356},"total_usd":0.715931,"stage1_batch_id":"msgbatch_011kfMfE81o6CTcyhVUqumuW","stage2_batch_id":"msgbatch_01DTputS6WNkH745x1nVSoBo","note":"batch pricing = 50% of standard","round2_stage1":{"model":"claude-sonnet-4-6","input_tokens":57227,"output_tokens":9460,"usd":0.15679},"round2_rules_fired":"R3","round2_stage2":{"model":"claude-opus-4-6","input_tokens":13536,"output_tokens":4161,"usd":0.257557}},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1986,\n      \"finding\": \"CD40 (Bp50) on B cells functions as a signal receptor that stimulates activated B cells to traverse the cell cycle; anti-Bp50 antibody augments B-cell proliferation when combined with B-cell activation signals, demonstrating a co-stimulatory role distinct from initial activation.\",\n      \"method\": \"Monoclonal antibody stimulation of purified resting and activated B cells with cell proliferation readout\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean functional antibody blocking experiment with defined proliferative phenotype, foundational paper replicated across the field\",\n      \"pmids\": [\"3487090\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"IL-6 induces phosphorylation of CD40, and this effect requires an intact CD40 cytoplasmic tail including threonine 234; reciprocally, CD40 cross-linking induces IL-6 production in B cells, establishing bidirectional signaling between IL-6 and CD40.\",\n      \"method\": \"Mutagenesis of CD40 cytoplasmic tail (tailless and T234A mutants), growth inhibition assays, phosphorylation assays in M12 transfectants and human B cells\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — site-directed mutagenesis with phosphorylation assay and functional rescue, multiple orthogonal readouts\",\n      \"pmids\": [\"1696597\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"CD40 is a 45–50 kDa glycoprotein member of the TNF receptor superfamily; its cytoplasmic domain lacks intrinsic kinase activity but its ligation by CD40L (a TNF superfamily member) drives B-cell proliferation, isotype switching, and generation of memory B cells.\",\n      \"method\": \"Molecular cloning, cross-linking assays with immobilized anti-CD40 or CD40L-expressing cells, isotype switching assays with cytokine combinations\",\n      \"journal\": \"Annual review of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — comprehensive review integrating multiple labs' functional reconstitution and genetic data; foundational structural and functional characterization\",\n      \"pmids\": [\"7516669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"TRAF3 (CRAF1) directly binds the CD40 cytoplasmic tail; the TRAF-C domain of CRAF1 is necessary and sufficient for CD40 binding and homodimerization; overexpression of a truncated CRAF1 inhibited CD40-mediated upregulation of CD23, identifying TRAF proteins as direct CD40 signal transducers.\",\n      \"method\": \"Yeast two-hybrid screen, overexpression of truncated dominant-negative CRAF1, CD23 upregulation assay\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — yeast two-hybrid identification plus dominant-negative functional validation; widely replicated finding\",\n      \"pmids\": [\"7533327\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"CD40 is expressed on vascular endothelial cells and its ligation by soluble CD40L (sgp39) activates endothelial cells, inducing E-selectin, ICAM-1, and augmenting VCAM-1 expression, leading to leukocyte adhesion; these effects are blocked by anti-CD40 mAb or soluble CD40.\",\n      \"method\": \"Recombinant soluble CD40L stimulation of endothelial cells, antibody blocking assays, cell adhesion assays, tissue immunostaining\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct ligand stimulation with blocking controls and multiple adhesion molecule readouts\",\n      \"pmids\": [\"7540655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"CD40L-dependent T cell activation requires CD40 signaling in antigen-presenting cells to upregulate B7 costimulatory molecules; reconstitution of CD40L-deficient mice with an activating anti-CD40 antibody that increased B7.2 expression restored full cellular and humoral immunity, placing CD40 upstream of the B7-CD28 axis.\",\n      \"method\": \"Genetic epistasis using CD40L-deficient mice, anti-CD40 antibody reconstitution, anti-B7 antibody blockade in wild-type mice\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean epistasis with genetic knockout and antibody rescue, multiple immune readouts\",\n      \"pmids\": [\"8791591\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Crystal structure of TRAF2 complexed with a CD40 cytoplasmic domain peptide at 2.4 Å resolution reveals that TRAF2 forms a mushroom-shaped trimer; CD40 peptide binds in an extended conformation in a groove on each TRAF monomer, with the spacing of three CD40 binding sites on the TRAF2 trimer complementary to trimeric CD40L-induced receptor clustering.\",\n      \"method\": \"X-ray crystallography (2.4 Å), functional peptide from CD40 cytoplasmic domain\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution crystal structure with functionally defined peptide; defines atomic mechanism of CD40-TRAF2 interaction\",\n      \"pmids\": [\"10411888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"TRAF5 is required for CD40-mediated B cell responses including proliferation and upregulation of CD23, CD54, CD80, CD86, and Fas; TRAF5-deficient B cells show substantially reduced Ig production in response to anti-CD40 plus IL-4, demonstrating TRAF5 as a component of the CD40 signaling complex.\",\n      \"method\": \"Gene targeting (TRAF5 knockout mice), B cell proliferation assays, surface molecule upregulation by flow cytometry, in vitro Ig production assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular phenotype across multiple readouts\",\n      \"pmids\": [\"10449775\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"CD40 trimerization is required for optimal NF-κB activation; trimeric CD40 cytoplasmic domains recruit a signaling complex containing TRAF2, TRAF3, TRAF5, TRAF6, and c-IAP1; c-IAP1 association is indirect and depends on an intact TRAF1/2/3 binding site on CD40.\",\n      \"method\": \"Expression of defined multimeric (dimeric and trimeric) soluble and myristoylated CD40 cytoplasmic domain constructs, NF-κB reporter assay, co-immunoprecipitation and isolation of signaling complexes\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reconstituted multimerization with defined point mutants plus biochemical complex isolation\",\n      \"pmids\": [\"11562359\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"CD40 generates multiple alternatively spliced mRNA isoforms whose expression is differentially regulated during macrophage and dendritic cell activation; three alternative isoforms disable CD40 signaling (measured by IL-12 p40 expression), and the major alternative isoform lacking the membrane endodomain reduces availability of signal-transducible CD40 on the cell surface, providing a post-transcriptional negative feedback mechanism.\",\n      \"method\": \"RT-PCR characterization of splice isoforms, IL-12 p40 reporter assay for signaling, activation time-course in macrophages and dendritic cells\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — functional reporter assay with multiple isoforms and mechanistic explanation; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"11172023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"The AT-hook transcription factor AKNA directly binds A/T-rich regulatory elements in the promoters of both CD40 and CD40L and coordinately regulates their expression; AKNA is predominantly expressed in germinal center B lymphocytes, T cells, NK cells, and dendritic cells.\",\n      \"method\": \"Promoter binding assays, identification of AKNA by molecular cloning, nuclear localization and expression profiling\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct promoter binding demonstrated with coordinate functional regulation of both receptor and ligand\",\n      \"pmids\": [\"11268217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"CD40 is expressed on neuronal cells and its expression increases during differentiation; CD40 ligation activates p44/42 MAPK, opposes JNK phosphorylation induced by NGF withdrawal, and protects neurons from apoptosis; CD40-deficient mice develop age-dependent neuronal dysfunction with decreased neurofilament, reduced Bcl-xL:Bax ratio, and increased DNA fragmentation.\",\n      \"method\": \"RT-PCR, western blot, immunofluorescence, MAPK activation assays, JNK assays, viability assays in N2a/PC12 cells, CD40 knockout mouse analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO phenotype plus in vitro signaling assays with multiple orthogonal readouts\",\n      \"pmids\": [\"11847112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Act1, a novel adaptor molecule, negatively regulates CD40 signaling in B cells; Act1-deficient B cells show increased CD40- and BAFF-mediated survival with stronger IκB phosphorylation, p100/p52 processing, and JNK/ERK/p38 activation; double knockout of CD40 and Act1 blocks the lymphoproliferative phenotype of Act1-deficient mice.\",\n      \"method\": \"Genetic deficiency (Act1 KO, B cell-specific Act1 KO, Act1/CD40 double KO mice), signaling assays for NF-κB, JNK, ERK, p38\",\n      \"journal\": \"Immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — epistasis with multiple KO combinations and defined signaling readouts\",\n      \"pmids\": [\"15485634\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CD40L mediates inflammation through interaction with the integrin Mac-1 independently of CD40; CD40L binds Mac-1 (demonstrated by flow cytometry, radioactive binding assays, and immunoprecipitation), leading to Mac-1-dependent adhesion, migration, and myeloperoxidase release.\",\n      \"method\": \"Flow cytometry, radioactive binding assays, immunoprecipitation, in vitro adhesion and migration assays, in vivo peritonitis model with CD40-deficient and CD40L-deficient mice\",\n      \"journal\": \"Circulation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple biochemical methods plus in vivo epistasis with separate KO lines\",\n      \"pmids\": [\"17372166\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Soluble CD40L binds directly to α5β1 integrin on monocytic cells in a CD40- and αIIbβ3-independent manner; this binding triggers translocation of α5β1 to detergent-insoluble fraction, rapid ERK1/2 activation, and IL-8 gene expression.\",\n      \"method\": \"Solid-phase binding assay with purified proteins, anti-CD40L/anti-α5β1 antibody blocking, Mn2+-mediated activation of α5β1, Triton X-100 fractionation, ERK1/2 phosphorylation assay, IL-8 reporter\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — purified protein direct binding plus multiple cell-based functional assays\",\n      \"pmids\": [\"17182621\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The CD40-TRAF6 signaling axis is the key regulator of neointima formation and vascular remodeling; mice with CD40 mutations at TRAF6 binding sites (but not TRAF2/3/5 binding sites) phenocopy CD40-deficient mice in reduced neointima, inflammatory cell infiltration, and impaired gelatinolytic/collagenolytic activity.\",\n      \"method\": \"Transgenic mice expressing CD40 with site-specific TRAF binding mutations, carotid artery ligation model, bone marrow reconstitution, intravital microscopy, in vitro leukocyte adhesion assays\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — elegant epistasis using point mutations in specific TRAF binding sites in vivo, replicated with bone marrow reconstitution\",\n      \"pmids\": [\"18195092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NEDD4 E3 ubiquitin ligase constitutively interacts with CD40 and mediates K63-linked ubiquitination of TRAF3; this TRAF3 ubiquitination is required for CD40-mediated AKT activation and modulates activation-induced cytidine deaminase expression and immunoglobulin class switch.\",\n      \"method\": \"Co-immunoprecipitation, K63-linked ubiquitination assay, NEDD4 knockdown, AKT activation assay, AID expression analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP plus K63-specific ubiquitination assay with functional AKT readout\",\n      \"pmids\": [\"25072696\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CD40 signaling in classical type 1 dendritic cells (cDC1s) induces Bcl2l1 (Bcl-xL) expression, which sustains cDC1 survival during antigen presentation to CD8+ T cells; cDC1-specific CD40 inactivation reduces mitochondrial transmembrane potential and increases caspase activation, reducing migratory cDC1 numbers; re-expression of Bcl2l1 rescues impaired antigen presentation by Cd40−/− cDC1s.\",\n      \"method\": \"Conditional cDC1-specific CD40 knockout, mitochondrial membrane potential assay, caspase activation assay, in vitro antigen presentation assay with Bcl2l1 re-expression rescue, in vivo tumor models\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — cell-type-specific KO with mechanistic rescue experiment and multiple orthogonal readouts\",\n      \"pmids\": [\"36271147\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"IL-2-activated human NK cells express CD40L, and recognition of CD40 on target cells provides an activation pathway for NK cell cytotoxicity; cross-linking of CD40L on NK cells induces redirected cytolysis; MHC class I expression on target cells can downregulate this CD40-dependent NK activation pathway.\",\n      \"method\": \"NK cell cytotoxicity assays with CD40-transfected target cells, anti-CD40 antibody blocking, cross-linking redirected cytolysis assay\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional cytotoxicity assays with antibody blocking and transfected targets; single lab\",\n      \"pmids\": [\"9182676\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"CD40 ligation on endothelial cells induces expression of angiogenesis factors including FGF-2, VEGF, Flt-1 and Flt-4; in vivo injection of CD40L-expressing fibroblasts into human skin engrafted on SCID mice triggers angiogenesis in a VEGF-dependent manner.\",\n      \"method\": \"Anti-CD40 antibody ligation of endothelial cells, in vivo SCID mouse human skin engraftment model, anti-VEGF blocking antibody\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro ligation plus in vivo model with antibody blocking; single lab\",\n      \"pmids\": [\"12874247\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"JAK3 associates with CD40 but is not essential for CD40-mediated B cell proliferation, IgE isotype switching, or upregulation of CD23, ICAM-1, CD80, and LT-α, as demonstrated by normal responses to CD40 stimulation in JAK3-deficient patients.\",\n      \"method\": \"Natural human genetic deficiency (JAK3-deficient patients), B cell stimulation assays, surface molecule upregulation\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — human genetic loss-of-function with multiple defined functional readouts; single study\",\n      \"pmids\": [\"9746783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Staphylococcal superantigens (TSST-1, SEB, SEC) stimulate chemokine (IL-8, MIP-3α) production from human vaginal epithelial cells through CD40; this was demonstrated using CRISPR-Cas9 CD40 knockout cells.\",\n      \"method\": \"CRISPR-Cas9 CD40 knockout in human vaginal epithelial cells, chemokine production assay\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean CRISPR KO with defined functional readout; single lab\",\n      \"pmids\": [\"30890614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"CD40-CD40L ligation stimulates B cell antigen processing; CD40 ligation reduces the amount of antigen and number of B cells required to activate an antigen-specific T cell hybrid, acting at an intracellular processing step rather than on peptide presentation, B7, LFA-1, or CD23 expression.\",\n      \"method\": \"Recombinant CD40L-expressing insect cells, anti-CD40 mAb, antigen-specific T cell hybrid activation assay, peptide presentation controls\",\n      \"journal\": \"European journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — defined functional assay with multiple controls; single lab\",\n      \"pmids\": [\"8566008\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CD40 is a TNF receptor superfamily member lacking intrinsic kinase activity that signals through its cytoplasmic tail by recruiting TRAF adapter proteins (TRAF2, TRAF3, TRAF5, TRAF6) upon trimerization induced by CD40L binding; TRAF6 is the key downstream mediator for inflammatory and vascular responses, while NEDD4-mediated K63-ubiquitination of TRAF3 links CD40 to AKT activation; CD40 signaling activates NF-κB, MAPK pathways, and Bcl-xL to promote antigen-presenting cell and B cell survival, costimulatory molecule upregulation, antigen processing, and isotype switching, with its activity regulated by alternatively spliced isoforms, the negative regulator Act1, and the transcription factor AKNA which coordinately controls CD40 and CD40L expression.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\nI'll classify each paper and extract discoveries only from KEEP papers.\n\n**Classification notes:**\n- Papers [14], [15], [20], [26], [35], [37], [40], [44], [51], [53], [54], [60], [67], [68], [73], [76], [80], [85], [87] from main corpus describe NF-κB p50, Raf/hsp90, or other proteins unrelated to CD40 → EXCLUDE\n- Additional papers [1],[2],[3],[6],[9],[10],[13],[15],[16],[17],[21],[24],[26] are GWAS/interactome studies with no CD40 mechanism → EXCLUDE\n- All remaining papers describe CD40 biology → KEEP\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1986,\n      \"finding\": \"CD40 (Bp50) is a 50-kDa cell-surface molecule on all B cells that delivers activation signals promoting B-cell progression through the cell cycle; anti-Bp50 monoclonal antibody augments proliferation of activated B cells but does not activate resting B cells alone, distinguishing it functionally from Bp35 (surface Ig).\",\n      \"method\": \"Monoclonal antibody stimulation assays on purified tonsillar B cells; cell-cycle analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean functional dissection with defined phenotypic readout, foundational paper replicated extensively\",\n      \"pmids\": [\"3487090\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1989,\n      \"finding\": \"CD40 (Bp50/CDw40) encodes a B-lymphocyte activation molecule whose predicted sequence shares extensive homology with the nerve growth factor receptor, placing it in the TNF receptor superfamily; its mRNA is induced by gamma-interferon in B cells and carcinomas.\",\n      \"method\": \"cDNA cloning, sequence analysis with transition matrix method, Northern blot\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — original molecular cloning and sequence analysis, foundational structural finding\",\n      \"pmids\": [\"2475341\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"IL-6 induces phosphorylation of CD40 in B cells through a mechanism requiring an intact CD40 cytoplasmic tail (including threonine-234), and conversely, CD40 ligation induces IL-6 production; this cross-talk requires functional CD40 but CD40 is not an IL-6 receptor.\",\n      \"method\": \"Mutagenesis of CD40 cytoplasmic tail (tailless and T234A mutants), growth inhibition assays, phosphorylation assays in M12 transformants\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — site-directed mutagenesis with functional readout in defined cell line, single lab\",\n      \"pmids\": [\"1696597\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"CD40 is a 45–50 kDa glycoprotein of 277 amino acids; its gene maps to human chromosome 20q11.2–q13.2. CD40 ligation drives B-cell proliferation, isotype switching (to IgE with IL-4/IL-13, to IgG3/IgG1/IgA1 with IL-10), and generation of long-term B-cell lines. Deficiency of CD40L underlies X-linked hyper-IgM syndrome.\",\n      \"method\": \"Biochemical characterization, gene mapping, B-cell culture assays with recombinant CD40L and cytokines\",\n      \"journal\": \"Annual review of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods, replicated across labs, comprehensive review synthesizing original experimental work\",\n      \"pmids\": [\"7516669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"gp39 (CD40L)–CD40 interactions are required for germinal center formation and generation of antigen-specific memory B cells in vivo; anti-gp39 antibody treatment completely abolished splenic germinal centers and blocked memory B-cell generation in adoptive transfer experiments.\",\n      \"method\": \"In vivo antibody blockade, immunohistochemistry, adoptive transfer experiments in mice\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic/antibody epistasis with defined in vivo phenotype, replicated\",\n      \"pmids\": [\"7516405\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Cyclosporin A (CsA) inhibits CD40L expression on T lymphocytes through calcineurin-dependent signaling: optimal CD40L expression requires protein kinase C activation and a rise in intracellular calcium; CsA inhibited IL-4-driven, CD40L-dependent IgE isotype switching.\",\n      \"method\": \"CsA analog dose-response correlating with calcineurin inhibition, T-cell activation assays, IgE switching assay\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — pharmacological dissection with calcineurin correlation, single lab\",\n      \"pmids\": [\"7907604\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"TRAF2 (via CRAF1) directly binds the CD40 cytoplasmic tail through a shared TRAF-C domain that is necessary and sufficient for both CD40 binding and homodimerization; overexpression of a truncated CRAF1 inhibited CD40-mediated upregulation of CD23, identifying TRAF proteins as CD40 signal transducers.\",\n      \"method\": \"Yeast two-hybrid screen, dominant-negative overexpression, CD23 upregulation assay\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — yeast two-hybrid plus dominant-negative functional validation, foundational discovery replicated by multiple labs\",\n      \"pmids\": [\"7533327\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"TRAF2-mediated NF-κB activation is a common signaling output of TNF-R2 and CD40; overexpression of TRAF2 is sufficient to induce NF-κB activation, and a dominant-negative TRAF2 (lacking the RING finger domain) blocks NF-κB activation by both receptors.\",\n      \"method\": \"Overexpression and dominant-negative experiments, NF-κB reporter assay\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — dominant-negative epistasis with defined molecular readout, replicated\",\n      \"pmids\": [\"7544915\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"CD40 is expressed on vascular endothelial cells and is upregulated by inflammatory agents; ligation by soluble gp39 (CD40L) activates endothelial cells to express E-selectin, ICAM-1, and augments VCAM-1 expression, promoting leukocyte adhesion.\",\n      \"method\": \"Flow cytometry, soluble recombinant CD40L stimulation, antibody blockade, adhesion assays, immunohistochemistry of inflammatory skin tissue\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods with functional readout, replicated\",\n      \"pmids\": [\"7540655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"CD40 is expressed on human umbilical vein endothelial cells and upregulated ~3-fold by TNF, IL-1, IFN-β, or IFN-γ; CD40 ligation by trimeric CD40L increases expression of E-selectin, VCAM-1, and ICAM-1 on endothelial cells.\",\n      \"method\": \"Flow cytometry, cytokine stimulation, recombinant trimeric CD40L ligation, adhesion molecule quantitation\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple cytokines tested, defined molecular readouts, replicated\",\n      \"pmids\": [\"7538666\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"CD40L-dependent T cell activation occurs through CD40 signaling on antigen-presenting cells that upregulates B7 costimulatory molecules (B7.2); reconstitution of CD40L-deficient mice with an activating anti-CD40 antibody restored both cellular and humoral immunity, which was then blocked by anti-B7 antibodies.\",\n      \"method\": \"CD40L-deficient mouse model, anti-CD40 agonist antibody reconstitution, anti-B7 blockade\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic reconstitution epistasis experiment with defined molecular pathway\",\n      \"pmids\": [\"8791591\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"CD40L (gp39)-positive helper T cells are co-localized with CD40-bearing monocytes/macrophages in active multiple sclerosis lesions; anti-CD40L monoclonal antibody prevented and treated experimental allergic encephalomyelitis (EAE) in mice, identifying CD40-CD40L as a functional mediator of CNS inflammation.\",\n      \"method\": \"Immunohistochemistry of MS brain sections, in vivo antibody blockade in EAE mouse model\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — combined human tissue analysis and functional in vivo intervention\",\n      \"pmids\": [\"8637903\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"A novel protein TRAF5 (originally identified as CRAF1 relative) binds the CD40 cytoplasmic tail; TRAF5-deficient B cells show defects in proliferation and upregulation of CD23, CD54, CD80, CD86, and Fas in response to CD40 stimulation, and reduced Ig production with IL-4.\",\n      \"method\": \"Gene targeting (TRAF5-/- mice), B-cell stimulation assays, surface molecule expression analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic knockout with multiple defined phenotypic readouts\",\n      \"pmids\": [\"10449775\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"CD40 on dendritic cells mediates T-lymphocyte activation in allogeneic mixed leukocyte reactions; cross-linking of CD40 on DCs markedly augments CD80 and CD86 expression, and CD40-CD40L co-stimulation of DCs has both CD80/CD86-dependent and -independent components.\",\n      \"method\": \"CD40-Ig fusion protein blockade, CD40L trimer cross-linking, MLR assay, flow cytometry\",\n      \"journal\": \"European journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional blockade and stimulation assays, single lab\",\n      \"pmids\": [\"8647193\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Platelets express CD40L within seconds of activation in vitro and during thrombus formation in vivo; platelet CD40L induces endothelial cells to secrete chemokines and express adhesion molecules, initiating an inflammatory response at sites of vessel injury.\",\n      \"method\": \"Flow cytometry, immunofluorescence, intravital microscopy, endothelial cell stimulation assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vitro and in vivo demonstration, multiple orthogonal methods, highly cited\",\n      \"pmids\": [\"9468137\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"IL-2-activated NK cells express CD40L and can kill CD40-expressing target cells through a CD40-dependent activation pathway; CD40L cross-linking on NK cells induces redirected cytolysis, and this pathway can be downregulated by MHC class I molecules on target cells.\",\n      \"method\": \"NK cell killing assays with CD40-transfected targets, anti-CD40 antibody blockade, CD40L cross-linking with redirected cytolysis\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional assays with antibody blockade and genetic controls, single lab\",\n      \"pmids\": [\"9182676\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"CD40L is constitutively expressed by human vascular endothelial cells, smooth muscle cells, and macrophages (not only activated T cells); these cell types co-express CD40 and CD40L in atherosclerotic lesions, enabling autocrine/paracrine signaling. CD40L on SMCs and macrophages is biologically active, inducing B7.2 on B cells and proinflammatory cytokines in SMCs.\",\n      \"method\": \"RT-PCR, immunohistochemistry, flow cytometry, B7.2 induction assay, cytokine ELISA\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple cell types, multiple methods, in vitro and in situ validation\",\n      \"pmids\": [\"9050882\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"CD40 signaling through CD40L-CD40 interactions is required for CTL priming by cross-presentation; signaling through CD40 on antigen-presenting cells can substitute for CD4+ T helper cell help in generating CD8+ cytotoxic T-cell responses.\",\n      \"method\": \"CD40L-deficient mice, agonistic anti-CD40 antibody reconstitution, CTL priming assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO plus antibody reconstitution epistasis, highly cited and replicated\",\n      \"pmids\": [\"9624004\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Anti-CD40L antibody treatment reduced atherosclerotic lesion size by 59% and lipid content by 79% in hyperlipidemic LDL-receptor-deficient mice, with significant decreases in macrophages (64%), T lymphocytes (70%), and VCAM-1 expression, establishing a causal role for CD40 signaling in atherogenesis in vivo.\",\n      \"method\": \"In vivo antibody blockade in LDL-receptor KO mice on high-cholesterol diet, morphometric analysis, immunohistochemistry\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic/pharmacological intervention with quantified molecular and cellular phenotypes, highly cited\",\n      \"pmids\": [\"9671306\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"TRAF6 binds a distinct region of the CD40 cytoplasmic domain (residues 230–245) that is separate from the TRAF2/3/5 binding site (residues 246–269); TRAF6 overexpression activates NF-κB, and its TRAF-C domain suppresses NF-κB activation triggered by CD40 lacking residues 246–277, indicating TRAF6 mediates a distinct CD40 signaling pathway.\",\n      \"method\": \"Yeast two-hybrid, deletion analysis, NF-κB reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — deletion mapping plus functional NF-κB assay, replicated by structural studies\",\n      \"pmids\": [\"8910514\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"RIP2 (a novel serine/threonine kinase with a CARD domain) is a component of the CD40 signaling complex; RIP2 overexpression activates NF-κB (requiring intact kinase domain plus CARD) and induces cell death (via CARD alone); RIP2 interacts with TRAF1, TRAF5, and TRAF6 but not TRAF2/3/4.\",\n      \"method\": \"Co-immunoprecipitation, overexpression, mutational analysis, NF-κB reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus mutagenesis with functional readout, single lab\",\n      \"pmids\": [\"9642260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Crystal structure (2.4 Å) of the TRAF2 receptor-binding fragment complexed with a CD40 cytoplasmic domain peptide reveals that TRAF2 forms a mushroom-shaped homotrimer; the CD40 peptide binds in an extended conformation with every side chain contacting a complementary groove on each TRAF monomer rim; spacing of CD40 binding sites on the TRAF2 trimer supports a signaling mechanism in which trimeric ligands pre-organize receptors to simultaneously engage three TRAF monomers.\",\n      \"method\": \"X-ray crystallography at 2.4 Å resolution\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — atomic resolution crystal structure of CD40-TRAF2 complex\",\n      \"pmids\": [\"10411888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"CD40 pre-mRNA is alternatively spliced to generate multiple isoforms; expression shifts from signal-transducible CD40 mRNA early in macrophage/DC activation to signal-nontransducible isoforms (accounting for ~50% of CD40 mRNA) at 24 h; three alternative isoforms can disable CD40 signaling, with the major isoform lacking the membrane-associated endodomain reducing full-length CD40 on the cell surface.\",\n      \"method\": \"RT-PCR, IL-12 p40 reporter assay for CD40 signaling, transfection of isoforms in macrophages and DCs\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional isoform analysis with reporter readout, single lab\",\n      \"pmids\": [\"11172023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"CD40 mRNA and protein are expressed by neuronal cells and are upregulated during differentiation; CD40 ligation in neuronal cells activates p44/42 MAPK and opposes JNK phosphorylation induced by NGF withdrawal, protecting neurons from injury; adult CD40-deficient mice show neuronal dysfunction with decreased neurofilament isoforms, reduced Bcl-xL:Bax ratio, and increased DNA fragmentation.\",\n      \"method\": \"RT-PCR, Western blot, immunofluorescence, MAPK activation assays, JNK assay, CD40 KO mouse analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple methods in vitro and KO phenotype in vivo, single lab\",\n      \"pmids\": [\"11847112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"AKNA, an AT-hook transcription factor, directly binds A/T-rich regulatory elements in the promoters of both CD40 and CD40L and coordinately regulates their expression; AKNA is a nuclear protein with PEST motifs expressed by germinal center B lymphocytes, T cells, NK cells, and DCs.\",\n      \"method\": \"Promoter binding assay, transfection, reporter gene assay, nuclear localization studies\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct promoter binding demonstrated, coordinate regulation shown, single lab\",\n      \"pmids\": [\"11268217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Act1 is a novel adaptor molecule that negatively regulates CD40 and BAFFR signaling; Act1-deficient B cells show significantly increased survival with stronger IκB phosphorylation, enhanced p100/p52 NF-κB2 processing, and augmented JNK, ERK, and p38 activation following CD40 stimulation; the B-cell phenotype in Act1-KO mice was largely rescued by double KO with CD40.\",\n      \"method\": \"Genetic knockout, double-knockout epistasis, B-cell signaling assays (NF-κB, MAPK pathways)\",\n      \"journal\": \"Immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with multiple orthogonal signaling readouts\",\n      \"pmids\": [\"15485634\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Crystal structures of TRAF6 alone and in complex with TRAF6-binding peptides from CD40 (and TRANCE-R) reveal a Pro-X-Glu-X-X-(aromatic/acidic) binding motif that differs fundamentally from TRAF2 peptide recognition (40° difference in bound peptide direction); cell-permeable peptides with this motif inhibit TRAF6 signaling.\",\n      \"method\": \"X-ray crystallography of TRAF6-CD40 peptide complex, cell-permeable peptide inhibition assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — atomic resolution crystal structure defining distinct CD40-TRAF6 interaction mechanism\",\n      \"pmids\": [\"12140561\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Soluble trimeric CD40 cytoplasmic domain constructs associate in complexes containing TRAF2, TRAF3, TRAF5, TRAF6, and c-IAP1; c-IAP1 association with the CD40 complex is indirect and dependent on an intact TRAF1/2/3 binding site; trimeric (but not monomeric) CD40 cytoplasmic domain is sufficient to activate NF-κB, indicating receptor trimerization is the minimal signaling unit.\",\n      \"method\": \"Soluble and myristoylated multimeric CD40 cytoplasmic domain constructs, immunoprecipitation, NF-κB reporter assay, point mutation analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstitution of signaling complexes with mutagenesis and functional readout\",\n      \"pmids\": [\"11562359\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"CD40 ligation on human endothelial cells induces expression of multiple angiogenesis factors including FGF-2, Flt-1, and Flt-4 in vitro; injection of CD40L-expressing fibroblasts into human skin grafts on SCID mice elicited angiogenesis factor expression and marked angiogenesis in vivo, which was abrogated by anti-VEGF, establishing a VEGF-dependent proangiogenic function of CD40 ligation.\",\n      \"method\": \"Anti-CD40 antibody stimulation of cultured ECs, in vivo SCID mouse skin graft model with CD40L-transfected fibroblasts, anti-VEGF blockade\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro and in vivo experiments with antibody blockade, single lab\",\n      \"pmids\": [\"12874247\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"CD40 ligation stimulates antigen processing by B cells, enhancing MHC class II-restricted antigen presentation to T-cell hybrids; CD40 acts at an intracellular processing step (not peptide presentation per se) and independently of effects on B7, LFA-1, or CD23 expression or B-cell proliferation.\",\n      \"method\": \"B-cell/T-cell hybrid co-culture assay, recombinant CD40L-expressing insect cells, anti-CD40 mAb, peptide presentation controls\",\n      \"journal\": \"European journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional dissection with multiple controls ruling out indirect mechanisms, single lab\",\n      \"pmids\": [\"8566008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"CD154 (CD40L) mRNA stability is regulated by a novel cis-acting instability element in a polypyrimidine-rich region of the 3'UTR; polypyrimidine tract-binding protein (PTB) family members bind this element, with PTB-T decreasing and PTB stabilizing CD154 3'UTR-dependent expression, identifying a post-transcriptional pathway controlling CD40L levels.\",\n      \"method\": \"RNA-protein pulldown/purification, mass spectrometry identification, reporter gene with tet-inducible system, cotransfection of PTB isoforms\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical purification of binding proteins plus functional reporter assays, single lab\",\n      \"pmids\": [\"12509450\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CD40L interacts directly with integrin Mac-1 (independently of CD40) via flow cytometry, radioactive binding assays, and immunoprecipitation, mediating Mac-1-dependent adhesion, migration, and myeloperoxidase release by inflammatory cells; CD40-deficient mice showed no reduction in atherosclerosis, whereas Mac-1 inhibition attenuated lesion development.\",\n      \"method\": \"Flow cytometry, radioactive binding assay, immunoprecipitation, in vitro adhesion/migration assays, CD40-KO and Mac-1 inhibition in LDL-receptor-KO mice\",\n      \"journal\": \"Circulation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal binding assays plus in vivo genetic/pharmacological validation\",\n      \"pmids\": [\"17372166\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Soluble CD40L (sCD40L) binds to α5β1 integrin on monocytic cells independently of CD40 and αIIbβ3; direct binding of sCD40L to purified α5β1 was confirmed by solid-phase binding assay; sCD40L binding triggers translocation of α5β1 to detergent-insoluble fraction, rapid ERK1/2 MAPK activation, and IL-8 gene expression.\",\n      \"method\": \"Solid-phase binding assay with purified α5β1, antibody inhibition, ERK1/2 phosphorylation assay, IL-8 gene expression\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct binding to purified protein plus signaling readout, identifies novel CD40L receptor\",\n      \"pmids\": [\"17182621\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The CD40–TRAF6 signaling axis is the key regulator of neointima formation and vascular remodeling; CD40 KO mice showed reduced neointima formation with decreased inflammatory cell infiltration and matrix protease activity; mice carrying CD40 transgenes with mutations at TRAF6 binding sites (but not TRAF2/3/5 binding sites) phenocopied CD40 KO, identifying CD40-TRAF6 as the critical downstream pathway.\",\n      \"method\": \"CD40-/- mouse model, bone marrow reconstitution, transgenic mice with site-specific TRAF-binding mutations, carotid ligation model, intravital microscopy\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with multiple transgenic lines carrying site-specific mutations\",\n      \"pmids\": [\"18195092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NEDD4 (an E3 ubiquitin ligase) constitutively interacts with CD40 and mediates K63-linked ubiquitination of TRAF3, which is required for CD40-mediated AKT kinase activation; NEDD4 also regulates immunoglobulin class switch by controlling activation-induced cytidine deaminase expression downstream of CD40.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay (K63-linkage specificity), AKT activation assay, class switch analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus ubiquitination assay with functional AKT readout, single lab\",\n      \"pmids\": [\"25072696\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Small molecules that block CD40–TRAF6 protein-protein interactions (identified by in silico docking and in vitro validation) reduce inflammation in peritonitis and sepsis mouse models without observed systemic side effects, validating the CD40-TRAF6 interface as a druggable target.\",\n      \"method\": \"In silico docking, in vitro binding assay, mouse models of peritonitis and sepsis\",\n      \"journal\": \"Journal of chemical information and modeling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — structure-based design validated in vitro and in vivo, single lab\",\n      \"pmids\": [\"25622654\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"miR-145 inhibits vascular smooth muscle cell (VSMC) proliferation by directly targeting CD40; overexpression of miR-145 significantly inhibited CD40 expression and VSMC differentiation/proliferation induced by TNF-α, TGF-β, and homocysteine, and decreased IL-6 levels in VSMC supernatants.\",\n      \"method\": \"miR-145 overexpression, siRNA-mediated CD40 knockdown, proliferation assays, IL-6 ELISA\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — functional KD with phenotypic readout but no direct binding validation of miR-145/CD40 interaction shown\",\n      \"pmids\": [\"27731400\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Staphylococcal superantigens (TSST-1, SEB, SEC) stimulate chemokine (IL-8, MIP-3α) production from human vaginal epithelial cells through CD40; CRISPR-Cas9 knockout of CD40 abolished this response, establishing CD40 as the receptor mediating superantigen-induced mucosal barrier disruption.\",\n      \"method\": \"CRISPR-Cas9 CD40 knockout, chemokine ELISA, superantigen stimulation assays\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — CRISPR KO with defined functional readout, single lab\",\n      \"pmids\": [\"30890614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CD40 signaling in classical type 1 dendritic cells (cDC1s) induces Bcl2l1 (Bcl-xL) expression, which sustains cDC1 survival (by maintaining mitochondrial transmembrane potential and suppressing caspase activation) during anti-tumor CD8 T-cell priming; cDC1-specific CD40 KO reduced migratory cDC1 numbers in tumor-draining lymph nodes, and this was reversed by Bcl2l1 re-expression.\",\n      \"method\": \"cDC1-specific Cre-driven CD40 KO, mitochondrial potential measurement, caspase activation assay, Bcl2l1 reconstitution, in vitro antigen presentation assay\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO with mechanistic rescue (Bcl2l1 reconstitution) and multiple orthogonal readouts\",\n      \"pmids\": [\"36271147\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"CD40 stimulation inhibits Fas- and TNF-receptor-mediated apoptosis in hepatocellular carcinoma cells in a dose-dependent manner by blocking activation of CPP32 (caspase-3).\",\n      \"method\": \"Anti-CD40 antibody stimulation, apoptosis assays, Western blot for CPP32 activation\",\n      \"journal\": \"Hepatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional assay with defined molecular mechanism (caspase-3 blockade), single lab\",\n      \"pmids\": [\"10498643\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"CD40 associates with JAK3 kinase; however, studies of JAK3-deficient patients show that JAK3 is not essential for CD40-mediated B-cell proliferation, IgE isotype switching, or upregulation of CD23, ICAM-1, CD80, and LT-α.\",\n      \"method\": \"B-cell stimulation assays in JAK3-deficient patient samples versus normal controls\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — natural human KO experiment with defined molecular readouts, single lab\",\n      \"pmids\": [\"9746783\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CD40 is a TNF receptor superfamily member (277 aa, ~50 kDa glycoprotein) that lacks intrinsic kinase activity but signals through its cytoplasmic tail by recruiting TRAF adaptor proteins (TRAF2/3/5 at residues 246–269 and TRAF6 at residues 230–245), which activate NF-κB, JNK/SAPK, and AKT pathways; receptor trimerization (driven by trimeric CD40L) is the minimal signaling unit, forming complexes that also include c-IAP1 and RIP2; downstream, NEDD4-mediated K63-ubiquitination of TRAF3 is required for AKT activation, Act1 negatively regulates signaling, and the TRAF6 axis specifically governs vascular inflammatory responses; beyond its canonical CD40L receptor, CD40L also signals through Mac-1 and α5β1 integrin; in dendritic cells CD40 induces Bcl2l1 to sustain survival during antigen presentation, and alternative splicing of CD40 pre-mRNA generates non-signaling isoforms that limit cellular responsiveness to CD40L.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CD40 is a TNF receptor superfamily member that functions as a central costimulatory receptor on B cells, dendritic cells, endothelial cells, and neurons, transducing signals from its ligand CD40L to drive adaptive immunity, vascular inflammation, and cell survival. Its cytoplasmic tail lacks intrinsic kinase activity but, upon ligand-induced trimerization, recruits TRAF adapter proteins (TRAF2, TRAF3, TRAF5, TRAF6, and indirectly c-IAP1) to activate NF-κB, MAPK (ERK, JNK, p38), and AKT pathways, with TRAF6 serving as the critical mediator of vascular remodeling and NEDD4-catalyzed K63-ubiquitination of TRAF3 linking CD40 to AKT activation and immunoglobulin class switching [PMID:7533327, PMID:11562359, PMID:18195092, PMID:25072696]. In dendritic cells, CD40 signaling induces Bcl-xL to sustain cDC1 survival during antigen cross-presentation to CD8+ T cells, while in B cells it drives proliferation, isotype switching, antigen processing, and costimulatory molecule upregulation, with the negative regulator Act1 restraining CD40-dependent NF-κB and MAPK activation [PMID:36271147, PMID:3487090, PMID:8566008, PMID:15485634]. CD40 activity is further tuned by alternatively spliced isoforms that reduce surface signaling-competent receptor and by the AT-hook transcription factor AKNA, which coordinately regulates both CD40 and CD40L promoters [PMID:11172023, PMID:11268217].\",\n  \"teleology\": [\n    {\n      \"year\": 1986,\n      \"claim\": \"Establishing that CD40 (Bp50) is a costimulatory receptor on B cells — not merely a surface marker — resolved whether the molecule had signaling function, demonstrating it drives activated B cell proliferation through the cell cycle.\",\n      \"evidence\": \"Anti-Bp50 monoclonal antibody stimulation of purified resting and activated B cells with proliferation readout\",\n      \"pmids\": [\"3487090\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ligand identity unknown\", \"Downstream signaling pathway uncharacterized\", \"Expression beyond B cells not tested\"]\n    },\n    {\n      \"year\": 1990,\n      \"claim\": \"Demonstration that CD40 undergoes IL-6-induced phosphorylation dependent on cytoplasmic tail residue T234 — and that CD40 ligation reciprocally induces IL-6 — established that the cytoplasmic domain is a signaling module despite lacking intrinsic kinase activity.\",\n      \"evidence\": \"Site-directed mutagenesis of CD40 cytoplasmic tail (tailless and T234A mutants) with phosphorylation and growth inhibition assays in M12 transfectants\",\n      \"pmids\": [\"1696597\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the kinase phosphorylating T234 unknown\", \"Adapter proteins mediating downstream signaling not identified\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Molecular cloning and functional reconstitution established CD40 as a TNF receptor superfamily member whose ligation by CD40L (a TNF family member) drives isotype switching and memory B cell generation, unifying its costimulatory role within a receptor family framework.\",\n      \"evidence\": \"Molecular cloning, cross-linking with CD40L-expressing cells, isotype switching assays\",\n      \"pmids\": [\"7516669\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Proximal signaling intermediates between CD40 and NF-κB not identified\", \"Structural basis of receptor–ligand interaction unknown\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Identification of TRAF3 as a direct binding partner of the CD40 cytoplasmic tail, and demonstration that CD40 ligation enhances antigen processing and activates endothelial cells to express adhesion molecules, extended the signaling mechanism to adapter recruitment and expanded CD40 function beyond B cells.\",\n      \"evidence\": \"Yeast two-hybrid screen for TRAF3, dominant-negative TRAF3 blocking CD23 upregulation; CD40L stimulation of endothelial cells with adhesion molecule readouts; antigen processing assay using T cell hybrid activation\",\n      \"pmids\": [\"7533327\", \"7540655\", \"8566008\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contributions of individual TRAF family members to distinct outputs unclear\", \"Structural details of TRAF–CD40 interaction lacking\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Genetic epistasis in CD40L-deficient mice demonstrated that CD40 signaling in APCs is upstream of B7 costimulatory molecule expression, positioning CD40 as a master switch for T cell help.\",\n      \"evidence\": \"Anti-CD40 antibody reconstitution of CD40L-knockout mice; anti-B7 antibody blockade in wild-type mice\",\n      \"pmids\": [\"8791591\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism linking CD40-TRAF signaling to B7 transcription not defined\", \"Contribution of individual TRAF members to B7 upregulation unknown\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"The 2.4 Å crystal structure of the TRAF2–CD40 peptide complex revealed a trimeric TRAF2 scaffold with three CD40-binding grooves spaced to match ligand-induced receptor trimerization, and TRAF5 knockout mice showed its requirement for CD40-mediated B cell proliferation and Ig production, establishing the structural and genetic basis of the multi-TRAF signaling platform.\",\n      \"evidence\": \"X-ray crystallography of TRAF2–CD40 complex; TRAF5-knockout B cell functional assays\",\n      \"pmids\": [\"10411888\", \"10449775\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TRAF2 versus TRAF5 versus TRAF6 binding is partitioned on the same receptor trimer unknown\", \"Crystal structure of full-length CD40 not available\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Reconstitution of defined CD40 multimers showed that trimerization is required for optimal NF-κB activation and assembly of a TRAF2/3/5/6 plus c-IAP1 signaling complex; concurrently, alternatively spliced CD40 isoforms were found to disable signaling, and the transcription factor AKNA was identified as a coordinator of both CD40 and CD40L expression — together defining the stoichiometric and transcriptional control layers of CD40 signaling.\",\n      \"evidence\": \"Multimeric CD40 cytoplasmic domain constructs with NF-κB reporters and co-IP; RT-PCR isoform characterization with IL-12 reporter; promoter binding assays for AKNA\",\n      \"pmids\": [\"11562359\", \"11172023\", \"11268217\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How alternative splicing is regulated by upstream signals unclear\", \"Whether AKNA is required in vivo for CD40/CD40L expression not tested genetically\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Discovery that CD40 is expressed on neurons and that its ligation activates ERK while opposing JNK-dependent apoptosis expanded CD40's role to neuronal survival, supported by age-dependent neurodegeneration in CD40-knockout mice.\",\n      \"evidence\": \"CD40 knockout mouse brain analysis, MAPK and JNK signaling assays in N2a/PC12 cells\",\n      \"pmids\": [\"11847112\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the physiological CD40L source in the CNS unclear\", \"Whether TRAF adapter usage in neurons mirrors that in immune cells unknown\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Identification of Act1 as a negative regulator of CD40 signaling — with Act1-deficient B cells showing hyperactive NF-κB, JNK, ERK, and p38, and the lymphoproliferative phenotype rescued by CD40 co-deletion — established a brake on the CD40-TRAF axis.\",\n      \"evidence\": \"Act1-knockout, Act1/CD40 double-knockout mice; NF-κB, JNK, ERK, p38 signaling assays\",\n      \"pmids\": [\"15485634\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which Act1 inhibits TRAF recruitment not defined\", \"Whether Act1 discriminates between TRAF2/3/5 and TRAF6 arms unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Transgenic mice bearing CD40 with site-specific TRAF-binding mutations demonstrated that the TRAF6-binding site, not the TRAF2/3/5-binding site, is the essential mediator of neointima formation and vascular inflammation, resolving which TRAF arm drives vascular pathology.\",\n      \"evidence\": \"Transgenic CD40 TRAF-binding mutant mice, carotid artery ligation model, bone marrow reconstitution, intravital microscopy\",\n      \"pmids\": [\"18195092\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TRAF6 specificity extends to other cardiovascular pathologies not tested\", \"Downstream effectors of the CD40-TRAF6 axis in vascular cells incompletely mapped\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Discovery that NEDD4 E3 ligase constitutively associates with CD40 and catalyzes K63-linked ubiquitination of TRAF3, which is required for AKT activation and immunoglobulin class switch, revealed a ubiquitin-dependent branch of CD40 signaling distinct from NF-κB.\",\n      \"evidence\": \"Co-immunoprecipitation of NEDD4 with CD40, K63-ubiquitination assay, NEDD4 knockdown with AKT activation and AID expression readout\",\n      \"pmids\": [\"25072696\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether NEDD4 ubiquitinates CD40 itself not resolved\", \"Structural basis for NEDD4–CD40 interaction unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Cell-type-specific CD40 deletion in cDC1s showed that CD40 signaling induces Bcl-xL to sustain dendritic cell survival during antigen cross-presentation, with Bcl-xL re-expression rescuing the defect, establishing a direct survival mechanism for antigen-presenting cell fitness.\",\n      \"evidence\": \"Conditional cDC1-specific CD40 knockout, mitochondrial membrane potential and caspase assays, Bcl2l1 re-expression rescue, in vivo tumor models\",\n      \"pmids\": [\"36271147\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Bcl-xL induction depends on TRAF6 or TRAF2/3/5 arm not distinguished\", \"Whether this survival mechanism extends to other DC subsets not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the CD40 cytoplasmic domain coordinates mutually exclusive versus simultaneous TRAF recruitment to direct divergent downstream outputs (NF-κB, AKT, MAPK, Bcl-xL) remains unresolved, as does the structural basis for full-length receptor signaling and the in vivo relevance of AKNA-mediated transcriptional coordination.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No full-length CD40 signalosome structure\", \"Quantitative TRAF competition model lacking\", \"In vivo requirement for AKNA in CD40/CD40L regulation not genetically validated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 1, 2, 5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 2, 4, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 2, 5, 7, 12, 17]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 8, 11, 15, 16]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [11, 17]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TRAF2\", \"TRAF3\", \"TRAF5\", \"TRAF6\", \"NEDD4\", \"TRAF1\", \"AKNA\"],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"CD40 is a TNF receptor superfamily member that functions as a master costimulatory receptor on B cells, dendritic cells, macrophages, and endothelial cells, coupling adaptive immune activation to vascular inflammation and antigen presentation. CD40 lacks intrinsic enzymatic activity and instead signals by recruiting TRAF adaptor proteins to two distinct cytoplasmic tail regions—TRAF2/3/5 bind residues 246–269 and TRAF6 binds residues 230–245—with trimeric receptor assembly as the minimal signaling unit that activates NF-κB, JNK/SAPK, p44/42 MAPK, and AKT pathways [PMID:7533327, PMID:8910514, PMID:11562359, PMID:10411888]. Functionally, CD40 ligation drives B-cell proliferation and immunoglobulin class switching, upregulates B7 costimulatory molecules on antigen-presenting cells to license T-cell priming, sustains dendritic cell survival via Bcl2l1 induction, and activates endothelial cells to express adhesion molecules and angiogenesis factors; the TRAF6 axis specifically governs vascular inflammatory remodeling [PMID:7516669, PMID:8791591, PMID:36271147, PMID:7540655, PMID:18195092]. Deficiency of its ligand CD40L causes X-linked hyper-IgM syndrome, and alternative splicing of CD40 pre-mRNA generates non-signaling isoforms that attenuate cellular responsiveness [PMID:7516669, PMID:11172023].\",\n  \"teleology\": [\n    {\n      \"year\": 1986,\n      \"claim\": \"Identification of CD40 (Bp50) as a B-cell surface molecule that delivers costimulatory activation signals established the gene's foundational role in B-cell biology, distinguishing it from surface immunoglobulin.\",\n      \"evidence\": \"Monoclonal antibody stimulation of purified tonsillar B cells with cell-cycle analysis\",\n      \"pmids\": [\"3487090\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular identity and sequence unknown\", \"Signaling mechanism uncharacterized\", \"Expression on non-B cells not investigated\"]\n    },\n    {\n      \"year\": 1989,\n      \"claim\": \"Molecular cloning of CD40 revealed homology to the nerve growth factor receptor, placing it in what became the TNF receptor superfamily and predicting a cytoplasmic signaling tail without intrinsic kinase activity.\",\n      \"evidence\": \"cDNA cloning and sequence analysis with transition matrix homology method\",\n      \"pmids\": [\"2475341\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ligand not yet identified\", \"Downstream signaling adaptors unknown\", \"Function of cytoplasmic tail not tested\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Functional studies established that CD40–CD40L interactions drive immunoglobulin class switching, germinal center formation, and memory B-cell generation in vivo, and that CD40L deficiency causes X-linked hyper-IgM syndrome, defining CD40 as essential for humoral immunity.\",\n      \"evidence\": \"In vivo anti-CD40L antibody blockade in mice, adoptive transfer, B-cell culture with recombinant CD40L and cytokines, human genetics\",\n      \"pmids\": [\"7516669\", \"7516405\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Intracellular signal transduction pathway unresolved\", \"Role in non-lymphoid tissues unclear\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Discovery that TRAF2 directly binds the CD40 cytoplasmic tail and mediates NF-κB activation identified the first signal-transduction mechanism downstream of CD40, explaining how a receptor without intrinsic kinase activity signals.\",\n      \"evidence\": \"Yeast two-hybrid, dominant-negative TRAF2 overexpression blocking CD40-induced CD23 and NF-κB reporter activation\",\n      \"pmids\": [\"7533327\", \"7544915\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Binding sites for other TRAF family members not mapped\", \"In vivo relevance of individual TRAFs untested\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Demonstration that CD40 is expressed and functional on vascular endothelial cells—where ligation induces E-selectin, VCAM-1, and ICAM-1—extended CD40 biology beyond the immune system into vascular inflammation.\",\n      \"evidence\": \"Flow cytometry, recombinant CD40L stimulation, adhesion assays on human endothelial cells\",\n      \"pmids\": [\"7540655\", \"7538666\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of TRAF pathways in endothelial vs. immune cells unknown\", \"In vivo vascular consequences not yet tested\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Mapping of TRAF6 to a distinct cytoplasmic domain region (residues 230–245, separate from TRAF2/3/5 at 246–269) revealed that CD40 engages two parallel TRAF signaling axes, each activating NF-κB through different mechanisms.\",\n      \"evidence\": \"Yeast two-hybrid deletion analysis and NF-κB reporter assays\",\n      \"pmids\": [\"8910514\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional distinction of TRAF6 vs. TRAF2/3/5 pathways in vivo not delineated\", \"Structural basis of TRAF6 recognition unknown\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"CD40 signaling on antigen-presenting cells was shown to upregulate B7 costimulatory molecules, providing the mechanistic link by which CD40L-expressing T helper cells license dendritic cells and macrophages for T-cell priming.\",\n      \"evidence\": \"CD40L-deficient mouse reconstitution with agonistic anti-CD40 antibody, anti-B7 blockade\",\n      \"pmids\": [\"8791591\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream survival signals in DCs not characterized\", \"Relative contribution of CD80 vs. CD86 unclear\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"In vivo antibody blockade of CD40L dramatically reduced atherosclerotic lesion formation in hyperlipidemic mice, establishing a causal role for the CD40–CD40L axis in atherogenesis beyond its immune functions.\",\n      \"evidence\": \"Anti-CD40L treatment in LDL-receptor KO mice on high-cholesterol diet with morphometry and immunohistochemistry\",\n      \"pmids\": [\"9671306\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether CD40 on immune cells or vascular cells drives atherogenesis not resolved\", \"Relative contribution of TRAF6 vs. TRAF2/3/5 in atherogenesis untested\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"The crystal structure of the TRAF2–CD40 peptide complex at 2.4 Å revealed the trimeric mushroom-shaped TRAF2 architecture and showed that each TRAF monomer rim binds one CD40 peptide in an extended conformation, providing the structural basis for ligand-induced receptor trimerization as the minimal signaling unit.\",\n      \"evidence\": \"X-ray crystallography at 2.4 Å resolution\",\n      \"pmids\": [\"10411888\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length receptor–TRAF complex structure unavailable\", \"Dynamics of signalosome assembly not captured\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Reconstitution experiments with soluble trimeric CD40 cytoplasmic domains showed that trimerization is sufficient for NF-κB activation and that the signaling complex contains TRAF2, TRAF3, TRAF5, TRAF6, and c-IAP1, defining the complete core signalosome composition.\",\n      \"evidence\": \"Myristoylated multimeric CD40 cytoplasmic domain constructs, immunoprecipitation, NF-κB reporter assay\",\n      \"pmids\": [\"11562359\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of TRAF molecules per CD40 trimer unknown\", \"Post-translational modifications of TRAFs in the complex not characterized\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Alternative splicing of CD40 pre-mRNA was found to generate non-signaling isoforms that accumulate during macrophage/DC activation, revealing a cell-intrinsic negative feedback mechanism that limits CD40 responsiveness over time.\",\n      \"evidence\": \"RT-PCR and IL-12 p40 reporter assay in macrophages and DCs transfected with individual isoforms\",\n      \"pmids\": [\"11172023\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Splicing factors controlling the switch not identified\", \"In vivo relevance of isoform ratio not demonstrated\", \"Whether isoforms act as dominant negatives at the cell surface or intracellularly not resolved\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"The TRAF6–CD40 crystal structure revealed a Pro-X-Glu-X-X-(aromatic/acidic) binding motif oriented 40° differently from TRAF2 peptide binding, providing the structural explanation for why TRAF6 engages a distinct CD40 cytoplasmic domain and enabling design of TRAF6-blocking peptides.\",\n      \"evidence\": \"X-ray crystallography of TRAF6–CD40 peptide complex, cell-permeable peptide inhibition\",\n      \"pmids\": [\"12140561\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether peptide inhibitors are selective in vivo unknown\", \"Cooperativity between TRAF2/3/5 and TRAF6 binding on the same receptor trimer not addressed\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Genetic epistasis using Act1-KO and Act1/CD40 double-KO mice identified Act1 as a negative regulator of CD40 signaling that restrains NF-κB processing, JNK, ERK, and p38 activation in B cells, establishing a cell-intrinsic brake on CD40 pathway output.\",\n      \"evidence\": \"Act1-KO and Act1/CD40 double-KO B-cell signaling assays\",\n      \"pmids\": [\"15485634\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which Act1 inhibits TRAF signaling not defined\", \"Act1 relevance in non-B-cell CD40 contexts untested\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"CD40L was shown to interact directly with integrin Mac-1 independently of CD40, mediating inflammatory cell adhesion and migration; Mac-1 inhibition—but not CD40 deficiency—attenuated atherosclerosis in vivo, revealing that some CD40L-driven vascular inflammation is CD40-independent.\",\n      \"evidence\": \"Multiple binding assays (flow cytometry, radioactive binding, co-IP) plus CD40-KO and Mac-1 inhibition in LDL-receptor KO mice\",\n      \"pmids\": [\"17372166\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of Mac-1 vs. α5β1 integrin in CD40L-independent signaling not compared\", \"Whether CD40L simultaneously engages CD40 and integrins on the same cell not tested\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Transgenic mice carrying CD40 with site-specific TRAF6-binding mutations phenocopied CD40-KO in neointima formation, while TRAF2/3/5-binding mutations did not, establishing the TRAF6 axis as the critical mediator of CD40-driven vascular inflammatory remodeling.\",\n      \"evidence\": \"TRAF-binding site mutant CD40 transgenic mice, carotid ligation model, bone marrow reconstitution\",\n      \"pmids\": [\"18195092\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TRAF6 pathway dominance is specific to vascular cells or generalizable not resolved\", \"Downstream effectors of TRAF6 in vascular remodeling not fully mapped\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"NEDD4 was identified as a constitutive CD40-associated E3 ubiquitin ligase that K63-ubiquitinates TRAF3, a modification required for CD40-mediated AKT activation and AID-dependent immunoglobulin class switching, adding a ubiquitin-dependent branch to CD40 signaling.\",\n      \"evidence\": \"Co-immunoprecipitation, K63-linkage-specific ubiquitination assay, AKT activation and class-switch analysis\",\n      \"pmids\": [\"25072696\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether NEDD4 also modifies other CD40-associated TRAFs not tested\", \"Structural basis of NEDD4–CD40 interaction unknown\", \"In vivo confirmation in NEDD4-conditional KO not performed\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Conditional deletion of CD40 in cDC1s revealed that CD40 sustains dendritic cell survival during anti-tumor T-cell priming by inducing Bcl2l1 (Bcl-xL), which maintains mitochondrial potential and blocks caspase activation—directly linking CD40 signaling to DC longevity in the tumor microenvironment.\",\n      \"evidence\": \"cDC1-specific Cre-driven CD40 KO, mitochondrial potential and caspase assays, Bcl2l1 reconstitution rescue\",\n      \"pmids\": [\"36271147\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Bcl2l1 induction operates through TRAF2/3/5 or TRAF6 not determined\", \"Relevance to non-tumor inflammatory DC survival unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: the structural basis of full-length CD40 signalosome assembly beyond peptide-level TRAF interactions; the cell-type-specific logic that determines TRAF6 vs. TRAF2/3/5 pathway dominance; the splicing regulators controlling non-signaling CD40 isoform production; and whether simultaneous CD40L engagement of CD40 and integrins on the same cell creates composite signaling outputs.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Full-length receptor–TRAF signalosome structure not solved\", \"Cell-type-specific TRAF pathway selection mechanism unknown\", \"Splicing factors regulating CD40 isoform switching not identified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 1, 3, 6, 7, 19]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [6, 19, 27]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1, 3, 8, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 4, 10, 17, 38]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6, 7, 19, 25, 27, 34]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [18, 33, 36]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [38, 39]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TRAF2\",\n      \"TRAF3\",\n      \"TRAF5\",\n      \"TRAF6\",\n      \"CD40LG\",\n      \"BIRC2\",\n      \"NEDD4\",\n      \"TRAF3IP2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}