{"gene":"CD47","run_date":"2026-04-28T17:28:52","timeline":{"discoveries":[{"year":2000,"finding":"CD47 functions as a 'marker of self' on red blood cells by binding to the inhibitory receptor SIRPα on macrophages, thereby preventing phagocytic clearance; CD47-deficient red blood cells are rapidly cleared by splenic red pulp macrophages.","method":"In vivo mouse model (CD47 knockout), functional phagocytosis assay, receptor binding","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular phenotype, replicated concept across multiple labs","pmids":["10856220"],"is_preprint":false},{"year":2001,"finding":"CD47 (IAP) is a receptor for thrombospondin family members and forms a supramolecular complex with specific integrins (beta1, beta2, beta3 families), heterotrimeric G proteins, and cholesterol; thrombospondin-derived VVM motif peptides act as CD47 agonists initiating Gi protein signaling to augment integrin function.","method":"Co-immunoprecipitation, functional assays (platelet activation, cell motility, adhesion)","journal":"Trends in Cell Biology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods reviewed, supported by primary data in PMID 10085089","pmids":["11306274","10085089"],"is_preprint":false},{"year":1999,"finding":"CD47 functionally couples to heterotrimeric Gi protein: CD47, its beta3 integrin partner, and Gi proteins form a stable detergent-soluble complex; GTP/AlF4 releases Gialpha from the complex and reduces CD47 agonist peptide binding; thrombospondin-derived 4N1K peptide stimulates GTPγS binding and decreases cAMP in a Gi-dependent manner.","method":"Immunoprecipitation, affinity chromatography, GTPγS binding assay, cAMP measurement, pertussis toxin inhibition","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1 — multiple in vitro biochemical assays with mechanistic controls","pmids":["10085089"],"is_preprint":false},{"year":2000,"finding":"CD47 interacts with SIRPα (MFR/P84/BIT/SHPS-1) via their amino-terminal immunoglobulin variable domains; this interaction mediates macrophage-macrophage adhesion and fusion leading to multinucleated giant cell formation.","method":"GST-CD47 fusion protein binding assay, Co-immunoprecipitation, antibody blocking of fusion, functional multinucleation assay","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — reconstituted binding with domain mapping and functional readout","pmids":["10964914"],"is_preprint":false},{"year":2009,"finding":"SIRPα binds CD47 and recruits tyrosine phosphatases SHP-1 and SHP-2 through its cytoplasmic region; the CD47-SIRPα interaction regulates cell migration and phagocytosis, and is important for immune homeostasis and neuronal network regulation.","method":"Biochemical binding assays, phosphorylation studies, functional migration/phagocytosis assays reviewed","journal":"Trends in Cell Biology","confidence":"High","confidence_rationale":"Tier 2 — extensively replicated signaling mechanism across multiple studies","pmids":["19144521"],"is_preprint":false},{"year":2016,"finding":"MYC transcription factor directly binds the promoters of CD47 and PD-L1 genes, regulating their expression; MYC inactivation reduces CD47 and PD-L1 protein and mRNA levels and enhances antitumor immune responses; enforced CD47 expression rescues tumor growth after MYC inactivation.","method":"ChIP (MYC binding to CD47 promoter), conditional MYC inactivation mouse models, shRNA knockdown, flow cytometry, qRT-PCR","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 — ChIP plus in vivo epistasis with enforced expression rescue experiments","pmids":["26966191"],"is_preprint":false},{"year":2007,"finding":"Species incompatibility of CD47 contributes to xenograft rejection: porcine CD47 fails to induce SIRPα tyrosine phosphorylation in human macrophages; soluble human CD47-Fc inhibits phagocytosis of porcine cells; transgenic expression of human CD47 on porcine cells reduces susceptibility to human macrophage phagocytosis.","method":"SIRPα phosphorylation assay, soluble CD47-Fc inhibition assay, transgenic CD47 expression with phagocytosis assay","journal":"PNAS","confidence":"High","confidence_rationale":"Tier 2 — multiple mechanistic experiments with phosphorylation readout and functional rescue","pmids":["17360380"],"is_preprint":false},{"year":2004,"finding":"CD47 forced expression in N1E-115 neuroblastoma cells induces neurite and filopodium formation through activation of Rac and Cdc42; SHPS-1-Fc (CD47 ligand) promotes this effect; neurite formation requires beta3 integrin; filopodium formation requires the entire CD47 structure whereas neurite formation requires only the extracellular region.","method":"Forced expression, dominant-negative Rac/Cdc42 inhibition, anti-beta3 antibody blocking, morphological quantification","journal":"Molecular Biology of the Cell","confidence":"High","confidence_rationale":"Tier 2 — domain dissection, GTPase inhibition, integrin antibody blocking with morphological readout","pmids":["15215311"],"is_preprint":false},{"year":1999,"finding":"Activation of specific epitopes on the Ig variable domain of CD47 rapidly induces apoptosis in T cells via a novel pathway independent of Fas, TNF receptor, CD3, CD4, CD45, p56lck, and classical DNA fragmentation; this CD47-mediated apoptosis is enhanced by CD3 co-ligation and requires T cell preactivation.","method":"Anti-CD47 monoclonal antibody (Ad22), flow cytometry (annexin V, PI), morphological analysis, variant Jurkat cell lines deficient in signaling molecules","journal":"Journal of Immunology","confidence":"Medium","confidence_rationale":"Tier 2 — signaling pathway exclusion via variant cell lines, single lab study","pmids":["10358145"],"is_preprint":false},{"year":2007,"finding":"CD47 interaction with thrombospondin-1/2 mediates T cell apoptosis via induction of BNIP3 (a proapoptotic Bcl-2 family member); CD47 physically interacts with BNIP3 and inhibits its proteasomal degradation, sensitizing activated T cells to CD47-induced apoptosis; CD47- or TSP-deficient mice show prolonged inflammation due to deficient T cell apoptosis.","method":"CD47-knockout and TSP-knockout mouse models, inflammation assay, co-immunoprecipitation of CD47-BNIP3, western blotting","journal":"Journal of Immunology","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse phenotype with molecular binding partner identification","pmids":["17442977"],"is_preprint":false},{"year":2004,"finding":"CD47 overexpression in cortical neurons enhances dendritic outgrowth and synaptic protein expression (synaptotagmin, syntaxin, synapsin I, SNAP25), increases glutamate release and Ca2+ oscillations; these effects require MAPK activation; CD47 siRNA knockdown reduces MAPK activity and synaptic protein levels.","method":"Viral gene transfer for overexpression, siRNA knockdown, MAPK activity assay, glutamate release measurement, Ca2+ imaging, western blotting","journal":"Journal of Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — gain- and loss-of-function with MAPK pathway mechanistic follow-up","pmids":["15297459"],"is_preprint":false},{"year":2004,"finding":"CD47 enhances alphavbeta3 integrin avidity through cholesterol-independent interactions; both CD47 and IgV-GPI (extracellular IgV domain with GPI anchor) increase the population of activatable integrin molecules and promote clustering of alphavbeta3; CD47, but not IgV-GPI, recruits alphavbeta3 to cholesterol-rich raft domains and enables Gi-dependent signaling.","method":"LIBS mAb binding (integrin activation reporter), chemical crosslinking, cholesterol depletion (methyl-beta-cyclodextrin), detergent-free raft fractionation","journal":"Journal of Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — domain dissection with multiple biochemical readouts in one study","pmids":["14966135"],"is_preprint":false},{"year":1995,"finding":"CD47 exists as four alternatively spliced forms differing only in their intracytoplasmic C-terminal tails; these splice forms are tissue-specifically expressed (form 2 on bone marrow-derived cells and endothelia, form 4 in brain/peripheral nervous system), and are evolutionarily conserved between mouse and human.","method":"PCR, isoform-specific polyclonal antibodies, immunohistochemistry, western blotting on tissue panels","journal":"Journal of Cell Science","confidence":"Medium","confidence_rationale":"Tier 2 — direct protein-level confirmation of splice forms with tissue-specific localization","pmids":["8586654"],"is_preprint":false},{"year":2012,"finding":"CD47 deficiency or blockade confers radioprotection by activating autophagic flux; irradiated CD47-deficient T cells and endothelial cells show increased autophagosome formation, elevated BECN1, ATG5, ATG7 and reduced SQSTM1/p62; pharmacological or siRNA inhibition of autophagy selectively sensitizes CD47-deficient cells to radiation; re-expression of CD47 reverses autophagic flux and radiation resistance.","method":"CD47 KO mice and cells, electron microscopy (autophagosome), LC3 puncta quantification, gene expression (BECN1, ATG5, ATG7, p62), siRNA, pharmacological autophagy inhibition, CD47 re-expression rescue","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods plus rescue experiment in single study","pmids":["22874555"],"is_preprint":false},{"year":2021,"finding":"SIRPα is expressed in NK cells and functions as an immune checkpoint; NK cell SIRPα is upregulated by IL-2 stimulation, interacts with target cell CD47 in a threshold-dependent manner, and counters NK stimulatory signals (IL-2, CD16, NKG2D); SIRPα deficiency or antibody blockade increases NK cell killing capacity; this axis is highly species-specific.","method":"NK cell SIRPα expression analysis, functional cytotoxicity assays, SIRPα KO, antibody blockade, xenogeneic target cell assays","journal":"Journal of Experimental Medicine","confidence":"High","confidence_rationale":"Tier 2 — KO and antibody blockade with functional cytotoxicity readout, multiple target cell types","pmids":["33416832"],"is_preprint":false},{"year":2018,"finding":"CD47 expression in the developing retinogeniculate system correlates with peak pruning periods; CD47-deficient mice exhibit increased microglial engulfment of retinogeniculate inputs and reduced synapse numbers; CD47 is required for neuronal-activity-mediated changes in engulfment—microglia in CD47-KO mice fail to preferentially engulf less active inputs.","method":"CD47-KO mice, immunofluorescence, confocal microscopy of synaptic engulfment, electrophysiology, activity manipulation","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 — KO with multiple readouts (morphological, electrophysiological) and activity-dependent functional link","pmids":["30308165"],"is_preprint":false},{"year":2023,"finding":"EGFR activation induces c-Src binding to CD47, leading to c-Src-mediated phosphorylation of CD47 at Y288; this phosphorylation inhibits the interaction between E3 ubiquitin ligase TRIM21 and CD47, blocking TRIM21-mediated K99/102 polyubiquitylation and proteasomal degradation of CD47; knock-in CD47 Y288F reduces CD47 levels and increases macrophage phagocytosis of tumor cells.","method":"Co-immunoprecipitation, mass spectrometry, site-directed mutagenesis (Y288F, K99/102R knock-in), ubiquitylation assay, phagocytosis assay, in vivo brain tumor model","journal":"Advanced Science","confidence":"High","confidence_rationale":"Tier 1-2 — PTM identification with mutagenesis validation, in vitro and in vivo functional readouts","pmids":["37541303"],"is_preprint":false},{"year":2023,"finding":"CD47/SIRPα axis downstream signaling requires deneddylation of SHP2: SHP2 is constitutively neddylated at K358 and K364 maintaining autoinhibition; upon CD47 ligation of SIRPα, SENP8 deneddylates SHP2, enabling dephosphorylation of substrates at the phagocytic cup and inhibiting macrophage phagocytosis.","method":"Mass spectrometry (neddylation site mapping), site-directed mutagenesis, SENP8 knockdown, phagocytosis assay, SHP2 activity assay","journal":"Journal of Clinical Investigation","confidence":"High","confidence_rationale":"Tier 1-2 — PTM site mapping with mutagenesis and enzymatic validation of mechanism","pmids":["36626230"],"is_preprint":false},{"year":2021,"finding":"Macrophage phagocytic decisions are regulated by the ratio of activating (FcγR) to inhibitory (SIRPα-CD47) signals over a broad range of absolute molecular densities; at least 10:1 activating:inhibitory ligand ratios are required to promote phagocytosis; SIRPα engagement reduces FcγR phosphorylation through inhibitory phosphatases recruited to CD47-bound SIRPα.","method":"Chimeric receptor reconstitution, quantitative ligand density control on model targets, FcγR phosphorylation assay, tumor cell phagocytosis assay","journal":"Cell Reports","confidence":"High","confidence_rationale":"Tier 1-2 — reconstituted receptor systems with quantitative signal integration and phosphorylation readout","pmids":["34433055"],"is_preprint":false},{"year":2005,"finding":"CD47 can induce intercellular adhesion and cell aggregation independent of active integrins and SIRPα, requiring Gi signaling (pertussis toxin-sensitive) and Rac GTPase activation; CD47-expressing cells preferentially bind other CD47-expressing cells; this CD47-mediated cell-cell adhesion modulates lymphocyte migration through fibroblast monolayers.","method":"Cell aggregation assay, pertussis toxin treatment, Clostridium difficile toxin B (Rho/Rac inhibitor), GTP-Rac pulldown, Jurkat transmigration assay","journal":"Journal of Cellular Physiology","confidence":"Medium","confidence_rationale":"Tier 2 — pharmacological pathway dissection with functional migration readout, single lab","pmids":["15880429"],"is_preprint":false},{"year":2017,"finding":"TNF-NF-κB1 signaling directly regulates CD47 expression by interacting with a constituent enhancer located within a CD47-associated super-enhancer specific to breast cancer; disruption of CD47 super-enhancers reduces CD47 gene expression.","method":"ChIP-seq, CRISPR-mediated enhancer deletion, luciferase reporter assay, TNF-α stimulation with NF-κB inhibition","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 2 — ChIP-seq with CRISPR functional validation and pathway intervention","pmids":["28378740"],"is_preprint":false},{"year":2018,"finding":"Chemotherapy-induced upregulation of CD47 is mediated by HIF transcription factors; genetic or pharmacological inhibition of HIFs blocks chemotherapy-induced enrichment of CD47+ breast cancer cells; hypoxic conditions also enrich CD47+ cells via HIF-dependent transcriptional induction.","method":"qRT-PCR, flow cytometry, HIF genetic knockdown (shRNA), pharmacological HIF inhibition, hypoxia treatment","journal":"PNAS","confidence":"Medium","confidence_rationale":"Tier 2 — genetic and pharmacological HIF inhibition with CD47 expression readout, single lab","pmids":["29367423"],"is_preprint":false},{"year":2022,"finding":"Extracellular vesicles from CD47-overexpressing cells can induce CD47 'cross-dressing' on recipient pig or human cells; cross-dressed CD47 interacts with SIRPα to inhibit phagocytosis; however, unlike autogenous CD47, ligation of cross-dressed CD47 does not transmit cell death signals.","method":"Extracellular vesicle transfer assay, SIRPα binding assay, phagocytosis assay, cell death assay after CD47 ligation","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 — functional dissection of autogenous vs. cross-dressed CD47 with multiple readouts, single lab","pmids":["36454036"],"is_preprint":false},{"year":2024,"finding":"Anti-CD47 antibodies cause rapid macrophage-mediated clearance of adoptively transferred CAR T cells; engineering CD47 variant Q31P (47E) on T cells engages SIRPα and provides a 'don't eat me' signal that is not blocked by anti-CD47 antibodies, protecting T cells from clearance while still enabling macrophage recruitment to tumors.","method":"In vivo CAR T cell clearance assay, CD47 variant engineering, anti-CD47 antibody treatment, tumor growth assay","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — in vivo functional rescue with engineered variant, multiple tumor models","pmids":["38750365"],"is_preprint":false},{"year":2020,"finding":"Infected cells upregulate CD47 as a host innate immune checkpoint response to pathogen recognition receptor (PRR) stimulation; CD47 upregulation slows phagocytic uptake and downstream APC functions; CD47 blockade or KO enhances immune responses during LCMV and M. tuberculosis infection; proinflammatory cytokines also upregulate CD47 on uninfected dendritic cells.","method":"PRR stimulation experiments, CD47-KO mice, antibody blockade, LCMV and M. tuberculosis infection models, flow cytometry","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 — KO and blockade with defined functional immune phenotypes across multiple infection models","pmids":["32576678"],"is_preprint":false}],"current_model":"CD47 is a multi-ligand, multi-domain transmembrane receptor that delivers a 'don't eat me' signal to SIRPα-expressing phagocytes (macrophages, dendritic cells, NK cells) by engaging SIRPα, which recruits SHP-1/SHP-2 (activated via SENP8-mediated deneddylation) to suppress phagocytic signaling; CD47 also forms complexes with beta-integrins and heterotrimeric Gi proteins to modulate cell adhesion, migration, and platelet activation, binds thrombospondin-1 to regulate T cell apoptosis and inflammation through a BNIP3-dependent pathway, is transcriptionally regulated by MYC, HIFs, TNF-NF-κB, and EGFR-c-Src signaling (the latter stabilizing CD47 by blocking TRIM21-mediated ubiquitylation and degradation), and protects synapses and specific cells from microglial/macrophage-mediated clearance in an activity-dependent manner."},"narrative":{"teleology":[{"year":1995,"claim":"Establishing that CD47 exists as four alternatively spliced isoforms with tissue-specific expression resolved how a single gene could serve distinct functions in brain, bone marrow, and epithelial compartments.","evidence":"PCR, isoform-specific antibodies, and immunohistochemistry on mouse and human tissue panels","pmids":["8586654"],"confidence":"Medium","gaps":["Functional differences between isoforms remain largely undefined","No structural basis for how cytoplasmic tail variants alter signaling"]},{"year":1999,"claim":"Demonstrating that CD47 physically couples to heterotrimeric Gi proteins and β3 integrin in a ternary complex, with thrombospondin-derived peptides stimulating GTPγS binding and cAMP reduction, established CD47 as a bona fide Gi-coupled co-receptor.","evidence":"Immunoprecipitation, affinity chromatography, GTPγS binding, cAMP measurement, and pertussis toxin inhibition in platelets and CHO cells","pmids":["10085089"],"confidence":"High","gaps":["Direct structural interface between CD47 multiply-spanning domain and Gαi not resolved","Stoichiometry of the CD47–integrin–Gi complex unknown"]},{"year":1999,"claim":"The finding that anti-CD47 antibodies induce a rapid, Fas/TNF-independent apoptotic pathway in activated T cells revealed a pro-death signaling capacity distinct from its integrin-modulatory function.","evidence":"Anti-CD47 mAb (Ad22), annexin V/PI staining, and signaling-deficient Jurkat variant panel","pmids":["10358145"],"confidence":"Medium","gaps":["Downstream death effectors not identified","Single antibody epitope; generalizability to physiological ligands unclear","Not independently replicated in primary T cells at that time"]},{"year":2000,"claim":"The discovery that CD47 knockout red blood cells are rapidly cleared by splenic macrophages established CD47 as a 'marker of self' and defined the foundational concept of a phagocytic checkpoint.","evidence":"CD47-knockout mice, in vivo RBC clearance assay, functional phagocytosis measurement","pmids":["10856220"],"confidence":"High","gaps":["Signaling cascade downstream of SIRPα in macrophages not yet mapped","Whether the checkpoint extends to nucleated cells was untested"]},{"year":2000,"claim":"Mapping the CD47–SIRPα interaction to their N-terminal IgV domains and linking it to macrophage fusion provided the structural basis for the inhibitory checkpoint and revealed a role in multinucleated giant cell formation.","evidence":"GST-CD47 fusion binding, co-immunoprecipitation, antibody blocking, multinucleation assay","pmids":["10964914"],"confidence":"High","gaps":["Atomic-resolution structure of the CD47–SIRPα interface not yet available","Signaling events connecting SIRPα engagement to fusion machinery unknown"]},{"year":2004,"claim":"Showing that CD47 enhances αvβ3 integrin avidity through both cholesterol-independent clustering and cholesterol-dependent raft recruitment, with only the latter enabling Gi signaling, dissected the dual mechanism by which CD47 modulates integrin function.","evidence":"LIBS mAb integrin activation reporter, chemical crosslinking, methyl-β-cyclodextrin raft disruption, detergent-free fractionation","pmids":["14966135"],"confidence":"Medium","gaps":["Identity of intermediate signaling molecules between CD47 raft recruitment and Gi activation unknown","Applicability to non-αvβ3 integrins untested at this resolution"]},{"year":2004,"claim":"CD47 overexpression in neurons promoted dendritic outgrowth and upregulated synaptic proteins via MAPK activation, establishing a neuronal signaling role beyond the immune checkpoint function.","evidence":"Viral overexpression, siRNA knockdown, MAPK assay, glutamate release and Ca²⁺ imaging in cortical neurons","pmids":["15297459"],"confidence":"Medium","gaps":["Which MAPK cascade member is directly activated by CD47 is unresolved","Relevance to in vivo synaptogenesis not yet shown at this point"]},{"year":2007,"claim":"Identification of BNIP3 as a CD47-binding proapoptotic effector that is stabilized by CD47 and mediates TSP-1-dependent T cell apoptosis provided a molecular mechanism for CD47-driven inflammation resolution.","evidence":"CD47-KO and TSP-KO mice, co-immunoprecipitation of CD47–BNIP3, inflammation assays","pmids":["17442977"],"confidence":"Medium","gaps":["Structural basis of the CD47–BNIP3 interaction not defined","Whether BNIP3 pathway operates in non-T cells expressing CD47 unknown"]},{"year":2007,"claim":"Demonstrating that porcine CD47 fails to trigger human SIRPα phosphorylation, while human CD47 expression on porcine cells rescues them from phagocytosis, established species specificity as a barrier in xenotransplantation.","evidence":"SIRPα phosphorylation assay, soluble CD47-Fc inhibition, transgenic human CD47 on porcine cells with phagocytosis readout","pmids":["17360380"],"confidence":"High","gaps":["Residues determining species specificity not fully mapped","In vivo xenograft survival benefit not quantified long-term"]},{"year":2009,"claim":"Consolidating evidence that SIRPα recruits SHP-1/SHP-2 through its cytoplasmic ITIMs upon CD47 ligation unified the phagocytic checkpoint, migration, and neuronal-network regulation under one signaling framework.","evidence":"Biochemical binding, phosphorylation studies, functional phagocytosis and migration assays reviewed","pmids":["19144521"],"confidence":"High","gaps":["Relative contributions of SHP-1 vs. SHP-2 in different cell types unresolved","Targets dephosphorylated at the phagocytic cup not catalogued"]},{"year":2012,"claim":"The observation that CD47 deficiency or blockade activates autophagic flux and confers radioprotection revealed that CD47 tonically suppresses autophagy, linking the checkpoint receptor to stress resistance.","evidence":"CD47-KO mice and cells, electron microscopy of autophagosomes, LC3/BECN1/ATG5/ATG7/p62 quantification, CD47 re-expression rescue","pmids":["22874555"],"confidence":"High","gaps":["Molecular mechanism by which CD47 suppresses autophagy initiation unknown","Whether autophagy regulation is SIRPα-dependent or cell-autonomous not distinguished"]},{"year":2016,"claim":"ChIP-validated binding of MYC to the CD47 promoter, with enforced CD47 expression rescuing tumor growth after MYC inactivation, established MYC as a direct transcriptional driver of immune evasion through CD47.","evidence":"ChIP, conditional MYC inactivation in mouse tumors, shRNA, flow cytometry, qRT-PCR, enforced CD47 rescue","pmids":["26966191"],"confidence":"High","gaps":["Whether MYC regulation of CD47 operates in non-transformed tissues unknown","Epigenetic co-factors at the CD47 promoter not identified"]},{"year":2017,"claim":"Identification of a TNF–NF-κB1-responsive constituent enhancer within a breast-cancer-specific CD47 super-enhancer revealed how inflammatory signaling amplifies CD47 transcription in a context-dependent manner.","evidence":"ChIP-seq, CRISPR enhancer deletion, luciferase reporter, TNF-α stimulation with NF-κB inhibition","pmids":["28378740"],"confidence":"High","gaps":["Whether this super-enhancer operates in non-breast cancer contexts untested","Transcription factor co-occupancy at the super-enhancer not fully mapped"]},{"year":2018,"claim":"Demonstrating that CD47-deficient mice exhibit excessive microglial engulfment of retinogeniculate synapses and fail to activity-dependently spare active inputs established CD47 as a neuronal 'don't eat me' signal that protects synapses during developmental pruning.","evidence":"CD47-KO mice, confocal engulfment imaging, electrophysiology, activity manipulation","pmids":["30308165"],"confidence":"High","gaps":["Whether microglial SIRPα is the cognate receptor in this context was assumed but not directly tested","Mechanism of activity-dependent CD47 regulation on individual synapses unknown"]},{"year":2021,"claim":"Quantitative reconstitution showing that macrophage phagocytic decisions depend on a ≥10:1 ratio of activating (FcγR) to inhibitory (SIRPα–CD47) signals, with SIRPα engagement suppressing FcγR phosphorylation, provided a biophysical framework for the checkpoint's signal integration logic.","evidence":"Chimeric receptor reconstitution, quantitative ligand density titration, FcγR phosphorylation assay","pmids":["34433055"],"confidence":"High","gaps":["Whether this ratio threshold applies in vivo with native receptor densities untested","Contributions of other 'eat me' and 'don't eat me' signals to the ratio not included"]},{"year":2021,"claim":"Discovery that NK cells express functional SIRPα that is upregulated by IL-2 and suppressed by CD47 on targets extended the CD47 checkpoint beyond myeloid phagocytes to innate lymphoid cytotoxicity.","evidence":"NK cell SIRPα expression analysis, cytotoxicity assays, SIRPα-KO, antibody blockade","pmids":["33416832"],"confidence":"High","gaps":["Downstream signaling events in NK cells after SIRPα–CD47 engagement not characterized","Whether this axis operates on all NK cell subsets unclear"]},{"year":2023,"claim":"Identification of EGFR–c-Src-mediated Y288 phosphorylation that blocks TRIM21-mediated K99/K102 polyubiquitylation and proteasomal degradation of CD47 revealed a post-translational stabilization mechanism exploited by tumors.","evidence":"Co-IP, mass spectrometry, Y288F and K99/102R knock-in mutagenesis, ubiquitylation and phagocytosis assays, in vivo brain tumor model","pmids":["37541303"],"confidence":"High","gaps":["Whether TRIM21-dependent CD47 degradation operates in non-EGFR-driven cancers unknown","Other kinases that may phosphorylate Y288 not surveyed"]},{"year":2023,"claim":"Demonstrating that SHP2 is constitutively neddylated at K358/K364 to maintain autoinhibition, and that SENP8-mediated deneddylation upon SIRPα engagement activates SHP2 at the phagocytic cup, resolved a missing step in CD47–SIRPα downstream signaling.","evidence":"Mass spectrometry neddylation-site mapping, site-directed mutagenesis, SENP8 knockdown, SHP2 activity and phagocytosis assays","pmids":["36626230"],"confidence":"High","gaps":["How SIRPα engagement triggers SENP8 recruitment or activation is unknown","Whether SHP1 is similarly regulated by neddylation untested"]},{"year":2024,"claim":"Engineering a CD47 variant (Q31P, '47E') that engages SIRPα but evades therapeutic anti-CD47 antibodies demonstrated that the checkpoint can be harnessed to protect adoptively transferred CAR T cells from macrophage clearance.","evidence":"In vivo CAR T cell clearance, CD47 variant engineering, anti-CD47 antibody treatment, multiple tumor models","pmids":["38750365"],"confidence":"High","gaps":["Long-term immunological consequences of 47E-expressing T cells in patients unknown","Whether 47E alters thrombospondin-1 binding or Gi signaling untested"]},{"year":null,"claim":"Key unresolved questions include: the structural basis for how CD47's multiply-spanning transmembrane domain couples to Gi proteins and integrins; the mechanism by which CD47 tonically suppresses autophagy; and how activity-dependent regulation of CD47 at individual synapses is achieved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structure of full-length CD47 in complex with Gi or integrin","Cell-autonomous vs. SIRPα-dependent signaling not fully dissected for autophagy regulation","Molecular link between neuronal activity and local CD47 surface expression at synapses unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0,3,4,14,18]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2,11]},{"term_id":"GO:0098631","term_label":"cell adhesion mediator activity","supporting_discovery_ids":[3,19]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1,3,11,16]}],"pathway":[],"complexes":["CD47–SIRPα","CD47–αvβ3 integrin–Gi"],"partners":["SIRPA","ITGB3","THBS1","GNAI2","BNIP3","TRIM21","SRC","SENP8"],"other_free_text":[]},"mechanistic_narrative":"CD47 is a broadly expressed transmembrane glycoprotein that functions as a central immune checkpoint and integrin co-receptor, integrating phagocytic inhibition, cell adhesion, and pro-apoptotic signaling across hematopoietic, neuronal, and vascular compartments. Its extracellular immunoglobulin variable (IgV) domain engages SIRPα on macrophages, dendritic cells, and NK cells, delivering a 'don't eat me' signal that suppresses phagocytosis through SENP8-mediated deneddylation and activation of SHP-1/SHP-2 phosphatases; this inhibitory axis operates ratiometrically against activating receptors such as FcγR and is species-specific [PMID:10856220, PMID:19144521, PMID:36626230, PMID:34433055, PMID:33416832]. CD47 simultaneously forms cholesterol-dependent supramolecular complexes with αvβ3 and other β-integrins and heterotrimeric Gi proteins, coupling thrombospondin-1 binding to cAMP reduction, Rac/Cdc42 activation, integrin avidity modulation, and cell migration [PMID:10085089, PMID:11306274, PMID:14966135, PMID:15215311]. CD47 surface levels are transcriptionally controlled by MYC, HIF, and TNF–NF-κB pathways and post-translationally stabilized by EGFR–c-Src phosphorylation at Y288, which blocks TRIM21-mediated ubiquitylation and proteasomal degradation; loss or blockade of CD47 enhances autophagic flux, confers radioprotection, and in the developing brain permits microglial engulfment of synapses in an activity-dependent manner [PMID:26966191, PMID:37541303, PMID:22874555, PMID:30308165]."},"prefetch_data":{"uniprot":{"accession":"Q08722","full_name":"Leukocyte surface antigen CD47","aliases":["Antigenic surface determinant protein OA3","Integrin-associated protein","IAP","Protein MER6"],"length_aa":323,"mass_kda":35.2,"function":"Adhesive protein that mediates cell-to-cell interactions (PubMed:11509594, PubMed:15383453). Acts as a receptor for thrombospondin THBS1 and as modulator of integrin signaling through the activation of heterotrimeric G proteins (PubMed:19004835, PubMed:7691831, PubMed:8550562). Involved in signal transduction, cardiovascular homeostasis, inflammation, apoptosis, angiogenesis, cellular self-renewal, and immunoregulation (PubMed:11509594, PubMed:15383453, PubMed:19004835, PubMed:27742621, PubMed:32679764, PubMed:7691831, PubMed:8550562). Plays a role in modulating pulmonary endothelin EDN1 signaling (PubMed:27742621). Modulates nitrous oxide (NO) signaling, in response to THBS1, hence playing a role as a pressor agent, supporting blood pressure (By similarity). Plays an important role in memory formation and synaptic plasticity in the hippocampus (By similarity). Receptor for SIRPA, binding to which prevents maturation of immature dendritic cells and inhibits cytokine production by mature dendritic cells (PubMed:11509594). Interaction with SIRPG mediates cell-cell adhesion, enhances superantigen-dependent T-cell-mediated proliferation and costimulates T-cell activation (PubMed:15383453). Positively modulates FAS-dependent apoptosis in T-cells, perhaps by enhancing FAS clustering (By similarity). Plays a role in suppressing angiogenesis and may be involved in metabolic dysregulation during normal aging (PubMed:32679764). In response to THBS1, negatively modulates wound healing (By similarity). Inhibits stem cell self-renewal, in response to THBS1, probably by regulation of the stem cell transcription factors POU5F1/OCT4, SOX2, MYC/c-Myc and KLF4 (By similarity). May play a role in membrane transport and/or integrin dependent signal transduction (PubMed:7691831). May prevent premature elimination of red blood cells (By similarity)","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q08722/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CD47","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CD47","total_profiled":1310},"omim":[{"mim_id":"610459","title":"PROLINE-RICH PROTEIN 13; PRR13","url":"https://www.omim.org/entry/610459"},{"mim_id":"606625","title":"SLAM FAMILY, MEMBER 7; SLAMF7","url":"https://www.omim.org/entry/606625"},{"mim_id":"605466","title":"SIGNAL REGULATORY PROTEIN, GAMMA; SIRPG","url":"https://www.omim.org/entry/605466"},{"mim_id":"605402","title":"CD274 MOLECULE; 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integrin-associated protein (IAP/CD47) in developing cortical neurons.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15297459","citation_count":31,"is_preprint":false},{"pmid":"25545814","id":"PMC_25545814","title":"IAP gene deletion and conditional knockout models.","date":"2014","source":"Seminars in cell & developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/25545814","citation_count":30,"is_preprint":false},{"pmid":"35436123","id":"PMC_35436123","title":"Recent Advances of Tumor Therapy Based on the CD47-SIRPα Axis.","date":"2022","source":"Molecular pharmaceutics","url":"https://pubmed.ncbi.nlm.nih.gov/35436123","citation_count":30,"is_preprint":false},{"pmid":"34056543","id":"PMC_34056543","title":"Insights into CD47/SIRPα axis-targeting tumor immunotherapy.","date":"2018","source":"Antibody therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/34056543","citation_count":30,"is_preprint":false},{"pmid":"29187357","id":"PMC_29187357","title":"IAP Antagonists Enhance Cytokine Production from Mouse and Human iNKT Cells.","date":"2017","source":"Cancer immunology research","url":"https://pubmed.ncbi.nlm.nih.gov/29187357","citation_count":30,"is_preprint":false},{"pmid":"36162554","id":"PMC_36162554","title":"Advantage of extracellular vesicles in hindering the CD47 signal for cancer immunotherapy.","date":"2022","source":"Journal of controlled release : official journal of the Controlled Release Society","url":"https://pubmed.ncbi.nlm.nih.gov/36162554","citation_count":29,"is_preprint":false},{"pmid":"34247273","id":"PMC_34247273","title":"Modulation of CD47-SIRPα innate immune checkpoint axis with Fc-function detuned anti-CD47 therapeutic antibody.","date":"2021","source":"Cancer immunology, immunotherapy : CII","url":"https://pubmed.ncbi.nlm.nih.gov/34247273","citation_count":29,"is_preprint":false},{"pmid":"36454036","id":"PMC_36454036","title":"CD47 cross-dressing by extracellular vesicles expressing CD47 inhibits phagocytosis without transmitting cell death signals.","date":"2022","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/36454036","citation_count":28,"is_preprint":false},{"pmid":"26914699","id":"PMC_26914699","title":"Enhanced biocompatibility of CD47-functionalized vascular stents.","date":"2016","source":"Biomaterials","url":"https://pubmed.ncbi.nlm.nih.gov/26914699","citation_count":28,"is_preprint":false},{"pmid":"16564725","id":"PMC_16564725","title":"Target cell CD47 regulates macrophage activation and erythrophagocytosis.","date":"2006","source":"Transfusion clinique et biologique : journal de la Societe francaise de transfusion sanguine","url":"https://pubmed.ncbi.nlm.nih.gov/16564725","citation_count":28,"is_preprint":false},{"pmid":"28693236","id":"PMC_28693236","title":"Significance of CD47 expression in gastric cancer.","date":"2017","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/28693236","citation_count":27,"is_preprint":false},{"pmid":"24382899","id":"PMC_24382899","title":"Pertussis vaccines: position paper of Indian Academy of Pediatrics (IAP).","date":"2013","source":"Indian pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/24382899","citation_count":26,"is_preprint":false},{"pmid":"32576628","id":"PMC_32576628","title":"Clinicopathological significance of CD47 expression in hepatocellular carcinoma.","date":"2020","source":"Journal of clinical pathology","url":"https://pubmed.ncbi.nlm.nih.gov/32576628","citation_count":26,"is_preprint":false},{"pmid":"34389694","id":"PMC_34389694","title":"Clinical Positioning of the IAP Antagonist Tolinapant (ASTX660) in Colorectal Cancer.","date":"2021","source":"Molecular cancer therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/34389694","citation_count":26,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":41104,"output_tokens":5896,"usd":0.105876},"stage2":{"model":"claude-opus-4-6","input_tokens":9592,"output_tokens":4583,"usd":0.243803},"total_usd":0.349679,"stage1_batch_id":"msgbatch_011kfMfE81o6CTcyhVUqumuW","stage2_batch_id":"msgbatch_01DTputS6WNkH745x1nVSoBo","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"CD47 functions as a 'marker of self' on red blood cells by binding to the inhibitory receptor SIRPα on macrophages, thereby preventing phagocytic clearance; CD47-deficient red blood cells are rapidly cleared by splenic red pulp macrophages.\",\n      \"method\": \"In vivo mouse model (CD47 knockout), functional phagocytosis assay, receptor binding\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular phenotype, replicated concept across multiple labs\",\n      \"pmids\": [\"10856220\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"CD47 (IAP) is a receptor for thrombospondin family members and forms a supramolecular complex with specific integrins (beta1, beta2, beta3 families), heterotrimeric G proteins, and cholesterol; thrombospondin-derived VVM motif peptides act as CD47 agonists initiating Gi protein signaling to augment integrin function.\",\n      \"method\": \"Co-immunoprecipitation, functional assays (platelet activation, cell motility, adhesion)\",\n      \"journal\": \"Trends in Cell Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods reviewed, supported by primary data in PMID 10085089\",\n      \"pmids\": [\"11306274\", \"10085089\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"CD47 functionally couples to heterotrimeric Gi protein: CD47, its beta3 integrin partner, and Gi proteins form a stable detergent-soluble complex; GTP/AlF4 releases Gialpha from the complex and reduces CD47 agonist peptide binding; thrombospondin-derived 4N1K peptide stimulates GTPγS binding and decreases cAMP in a Gi-dependent manner.\",\n      \"method\": \"Immunoprecipitation, affinity chromatography, GTPγS binding assay, cAMP measurement, pertussis toxin inhibition\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple in vitro biochemical assays with mechanistic controls\",\n      \"pmids\": [\"10085089\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"CD47 interacts with SIRPα (MFR/P84/BIT/SHPS-1) via their amino-terminal immunoglobulin variable domains; this interaction mediates macrophage-macrophage adhesion and fusion leading to multinucleated giant cell formation.\",\n      \"method\": \"GST-CD47 fusion protein binding assay, Co-immunoprecipitation, antibody blocking of fusion, functional multinucleation assay\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — reconstituted binding with domain mapping and functional readout\",\n      \"pmids\": [\"10964914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SIRPα binds CD47 and recruits tyrosine phosphatases SHP-1 and SHP-2 through its cytoplasmic region; the CD47-SIRPα interaction regulates cell migration and phagocytosis, and is important for immune homeostasis and neuronal network regulation.\",\n      \"method\": \"Biochemical binding assays, phosphorylation studies, functional migration/phagocytosis assays reviewed\",\n      \"journal\": \"Trends in Cell Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — extensively replicated signaling mechanism across multiple studies\",\n      \"pmids\": [\"19144521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"MYC transcription factor directly binds the promoters of CD47 and PD-L1 genes, regulating their expression; MYC inactivation reduces CD47 and PD-L1 protein and mRNA levels and enhances antitumor immune responses; enforced CD47 expression rescues tumor growth after MYC inactivation.\",\n      \"method\": \"ChIP (MYC binding to CD47 promoter), conditional MYC inactivation mouse models, shRNA knockdown, flow cytometry, qRT-PCR\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP plus in vivo epistasis with enforced expression rescue experiments\",\n      \"pmids\": [\"26966191\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Species incompatibility of CD47 contributes to xenograft rejection: porcine CD47 fails to induce SIRPα tyrosine phosphorylation in human macrophages; soluble human CD47-Fc inhibits phagocytosis of porcine cells; transgenic expression of human CD47 on porcine cells reduces susceptibility to human macrophage phagocytosis.\",\n      \"method\": \"SIRPα phosphorylation assay, soluble CD47-Fc inhibition assay, transgenic CD47 expression with phagocytosis assay\",\n      \"journal\": \"PNAS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple mechanistic experiments with phosphorylation readout and functional rescue\",\n      \"pmids\": [\"17360380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"CD47 forced expression in N1E-115 neuroblastoma cells induces neurite and filopodium formation through activation of Rac and Cdc42; SHPS-1-Fc (CD47 ligand) promotes this effect; neurite formation requires beta3 integrin; filopodium formation requires the entire CD47 structure whereas neurite formation requires only the extracellular region.\",\n      \"method\": \"Forced expression, dominant-negative Rac/Cdc42 inhibition, anti-beta3 antibody blocking, morphological quantification\",\n      \"journal\": \"Molecular Biology of the Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — domain dissection, GTPase inhibition, integrin antibody blocking with morphological readout\",\n      \"pmids\": [\"15215311\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Activation of specific epitopes on the Ig variable domain of CD47 rapidly induces apoptosis in T cells via a novel pathway independent of Fas, TNF receptor, CD3, CD4, CD45, p56lck, and classical DNA fragmentation; this CD47-mediated apoptosis is enhanced by CD3 co-ligation and requires T cell preactivation.\",\n      \"method\": \"Anti-CD47 monoclonal antibody (Ad22), flow cytometry (annexin V, PI), morphological analysis, variant Jurkat cell lines deficient in signaling molecules\",\n      \"journal\": \"Journal of Immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — signaling pathway exclusion via variant cell lines, single lab study\",\n      \"pmids\": [\"10358145\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CD47 interaction with thrombospondin-1/2 mediates T cell apoptosis via induction of BNIP3 (a proapoptotic Bcl-2 family member); CD47 physically interacts with BNIP3 and inhibits its proteasomal degradation, sensitizing activated T cells to CD47-induced apoptosis; CD47- or TSP-deficient mice show prolonged inflammation due to deficient T cell apoptosis.\",\n      \"method\": \"CD47-knockout and TSP-knockout mouse models, inflammation assay, co-immunoprecipitation of CD47-BNIP3, western blotting\",\n      \"journal\": \"Journal of Immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse phenotype with molecular binding partner identification\",\n      \"pmids\": [\"17442977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"CD47 overexpression in cortical neurons enhances dendritic outgrowth and synaptic protein expression (synaptotagmin, syntaxin, synapsin I, SNAP25), increases glutamate release and Ca2+ oscillations; these effects require MAPK activation; CD47 siRNA knockdown reduces MAPK activity and synaptic protein levels.\",\n      \"method\": \"Viral gene transfer for overexpression, siRNA knockdown, MAPK activity assay, glutamate release measurement, Ca2+ imaging, western blotting\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — gain- and loss-of-function with MAPK pathway mechanistic follow-up\",\n      \"pmids\": [\"15297459\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"CD47 enhances alphavbeta3 integrin avidity through cholesterol-independent interactions; both CD47 and IgV-GPI (extracellular IgV domain with GPI anchor) increase the population of activatable integrin molecules and promote clustering of alphavbeta3; CD47, but not IgV-GPI, recruits alphavbeta3 to cholesterol-rich raft domains and enables Gi-dependent signaling.\",\n      \"method\": \"LIBS mAb binding (integrin activation reporter), chemical crosslinking, cholesterol depletion (methyl-beta-cyclodextrin), detergent-free raft fractionation\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — domain dissection with multiple biochemical readouts in one study\",\n      \"pmids\": [\"14966135\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"CD47 exists as four alternatively spliced forms differing only in their intracytoplasmic C-terminal tails; these splice forms are tissue-specifically expressed (form 2 on bone marrow-derived cells and endothelia, form 4 in brain/peripheral nervous system), and are evolutionarily conserved between mouse and human.\",\n      \"method\": \"PCR, isoform-specific polyclonal antibodies, immunohistochemistry, western blotting on tissue panels\",\n      \"journal\": \"Journal of Cell Science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct protein-level confirmation of splice forms with tissue-specific localization\",\n      \"pmids\": [\"8586654\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CD47 deficiency or blockade confers radioprotection by activating autophagic flux; irradiated CD47-deficient T cells and endothelial cells show increased autophagosome formation, elevated BECN1, ATG5, ATG7 and reduced SQSTM1/p62; pharmacological or siRNA inhibition of autophagy selectively sensitizes CD47-deficient cells to radiation; re-expression of CD47 reverses autophagic flux and radiation resistance.\",\n      \"method\": \"CD47 KO mice and cells, electron microscopy (autophagosome), LC3 puncta quantification, gene expression (BECN1, ATG5, ATG7, p62), siRNA, pharmacological autophagy inhibition, CD47 re-expression rescue\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods plus rescue experiment in single study\",\n      \"pmids\": [\"22874555\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SIRPα is expressed in NK cells and functions as an immune checkpoint; NK cell SIRPα is upregulated by IL-2 stimulation, interacts with target cell CD47 in a threshold-dependent manner, and counters NK stimulatory signals (IL-2, CD16, NKG2D); SIRPα deficiency or antibody blockade increases NK cell killing capacity; this axis is highly species-specific.\",\n      \"method\": \"NK cell SIRPα expression analysis, functional cytotoxicity assays, SIRPα KO, antibody blockade, xenogeneic target cell assays\",\n      \"journal\": \"Journal of Experimental Medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO and antibody blockade with functional cytotoxicity readout, multiple target cell types\",\n      \"pmids\": [\"33416832\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CD47 expression in the developing retinogeniculate system correlates with peak pruning periods; CD47-deficient mice exhibit increased microglial engulfment of retinogeniculate inputs and reduced synapse numbers; CD47 is required for neuronal-activity-mediated changes in engulfment—microglia in CD47-KO mice fail to preferentially engulf less active inputs.\",\n      \"method\": \"CD47-KO mice, immunofluorescence, confocal microscopy of synaptic engulfment, electrophysiology, activity manipulation\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO with multiple readouts (morphological, electrophysiological) and activity-dependent functional link\",\n      \"pmids\": [\"30308165\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"EGFR activation induces c-Src binding to CD47, leading to c-Src-mediated phosphorylation of CD47 at Y288; this phosphorylation inhibits the interaction between E3 ubiquitin ligase TRIM21 and CD47, blocking TRIM21-mediated K99/102 polyubiquitylation and proteasomal degradation of CD47; knock-in CD47 Y288F reduces CD47 levels and increases macrophage phagocytosis of tumor cells.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, site-directed mutagenesis (Y288F, K99/102R knock-in), ubiquitylation assay, phagocytosis assay, in vivo brain tumor model\",\n      \"journal\": \"Advanced Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — PTM identification with mutagenesis validation, in vitro and in vivo functional readouts\",\n      \"pmids\": [\"37541303\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CD47/SIRPα axis downstream signaling requires deneddylation of SHP2: SHP2 is constitutively neddylated at K358 and K364 maintaining autoinhibition; upon CD47 ligation of SIRPα, SENP8 deneddylates SHP2, enabling dephosphorylation of substrates at the phagocytic cup and inhibiting macrophage phagocytosis.\",\n      \"method\": \"Mass spectrometry (neddylation site mapping), site-directed mutagenesis, SENP8 knockdown, phagocytosis assay, SHP2 activity assay\",\n      \"journal\": \"Journal of Clinical Investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — PTM site mapping with mutagenesis and enzymatic validation of mechanism\",\n      \"pmids\": [\"36626230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Macrophage phagocytic decisions are regulated by the ratio of activating (FcγR) to inhibitory (SIRPα-CD47) signals over a broad range of absolute molecular densities; at least 10:1 activating:inhibitory ligand ratios are required to promote phagocytosis; SIRPα engagement reduces FcγR phosphorylation through inhibitory phosphatases recruited to CD47-bound SIRPα.\",\n      \"method\": \"Chimeric receptor reconstitution, quantitative ligand density control on model targets, FcγR phosphorylation assay, tumor cell phagocytosis assay\",\n      \"journal\": \"Cell Reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — reconstituted receptor systems with quantitative signal integration and phosphorylation readout\",\n      \"pmids\": [\"34433055\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"CD47 can induce intercellular adhesion and cell aggregation independent of active integrins and SIRPα, requiring Gi signaling (pertussis toxin-sensitive) and Rac GTPase activation; CD47-expressing cells preferentially bind other CD47-expressing cells; this CD47-mediated cell-cell adhesion modulates lymphocyte migration through fibroblast monolayers.\",\n      \"method\": \"Cell aggregation assay, pertussis toxin treatment, Clostridium difficile toxin B (Rho/Rac inhibitor), GTP-Rac pulldown, Jurkat transmigration assay\",\n      \"journal\": \"Journal of Cellular Physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — pharmacological pathway dissection with functional migration readout, single lab\",\n      \"pmids\": [\"15880429\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TNF-NF-κB1 signaling directly regulates CD47 expression by interacting with a constituent enhancer located within a CD47-associated super-enhancer specific to breast cancer; disruption of CD47 super-enhancers reduces CD47 gene expression.\",\n      \"method\": \"ChIP-seq, CRISPR-mediated enhancer deletion, luciferase reporter assay, TNF-α stimulation with NF-κB inhibition\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-seq with CRISPR functional validation and pathway intervention\",\n      \"pmids\": [\"28378740\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Chemotherapy-induced upregulation of CD47 is mediated by HIF transcription factors; genetic or pharmacological inhibition of HIFs blocks chemotherapy-induced enrichment of CD47+ breast cancer cells; hypoxic conditions also enrich CD47+ cells via HIF-dependent transcriptional induction.\",\n      \"method\": \"qRT-PCR, flow cytometry, HIF genetic knockdown (shRNA), pharmacological HIF inhibition, hypoxia treatment\",\n      \"journal\": \"PNAS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic and pharmacological HIF inhibition with CD47 expression readout, single lab\",\n      \"pmids\": [\"29367423\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Extracellular vesicles from CD47-overexpressing cells can induce CD47 'cross-dressing' on recipient pig or human cells; cross-dressed CD47 interacts with SIRPα to inhibit phagocytosis; however, unlike autogenous CD47, ligation of cross-dressed CD47 does not transmit cell death signals.\",\n      \"method\": \"Extracellular vesicle transfer assay, SIRPα binding assay, phagocytosis assay, cell death assay after CD47 ligation\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional dissection of autogenous vs. cross-dressed CD47 with multiple readouts, single lab\",\n      \"pmids\": [\"36454036\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Anti-CD47 antibodies cause rapid macrophage-mediated clearance of adoptively transferred CAR T cells; engineering CD47 variant Q31P (47E) on T cells engages SIRPα and provides a 'don't eat me' signal that is not blocked by anti-CD47 antibodies, protecting T cells from clearance while still enabling macrophage recruitment to tumors.\",\n      \"method\": \"In vivo CAR T cell clearance assay, CD47 variant engineering, anti-CD47 antibody treatment, tumor growth assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo functional rescue with engineered variant, multiple tumor models\",\n      \"pmids\": [\"38750365\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Infected cells upregulate CD47 as a host innate immune checkpoint response to pathogen recognition receptor (PRR) stimulation; CD47 upregulation slows phagocytic uptake and downstream APC functions; CD47 blockade or KO enhances immune responses during LCMV and M. tuberculosis infection; proinflammatory cytokines also upregulate CD47 on uninfected dendritic cells.\",\n      \"method\": \"PRR stimulation experiments, CD47-KO mice, antibody blockade, LCMV and M. tuberculosis infection models, flow cytometry\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO and blockade with defined functional immune phenotypes across multiple infection models\",\n      \"pmids\": [\"32576678\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CD47 is a multi-ligand, multi-domain transmembrane receptor that delivers a 'don't eat me' signal to SIRPα-expressing phagocytes (macrophages, dendritic cells, NK cells) by engaging SIRPα, which recruits SHP-1/SHP-2 (activated via SENP8-mediated deneddylation) to suppress phagocytic signaling; CD47 also forms complexes with beta-integrins and heterotrimeric Gi proteins to modulate cell adhesion, migration, and platelet activation, binds thrombospondin-1 to regulate T cell apoptosis and inflammation through a BNIP3-dependent pathway, is transcriptionally regulated by MYC, HIFs, TNF-NF-κB, and EGFR-c-Src signaling (the latter stabilizing CD47 by blocking TRIM21-mediated ubiquitylation and degradation), and protects synapses and specific cells from microglial/macrophage-mediated clearance in an activity-dependent manner.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CD47 is a broadly expressed transmembrane glycoprotein that functions as a central immune checkpoint and integrin co-receptor, integrating phagocytic inhibition, cell adhesion, and pro-apoptotic signaling across hematopoietic, neuronal, and vascular compartments. Its extracellular immunoglobulin variable (IgV) domain engages SIRPα on macrophages, dendritic cells, and NK cells, delivering a 'don't eat me' signal that suppresses phagocytosis through SENP8-mediated deneddylation and activation of SHP-1/SHP-2 phosphatases; this inhibitory axis operates ratiometrically against activating receptors such as FcγR and is species-specific [PMID:10856220, PMID:19144521, PMID:36626230, PMID:34433055, PMID:33416832]. CD47 simultaneously forms cholesterol-dependent supramolecular complexes with αvβ3 and other β-integrins and heterotrimeric Gi proteins, coupling thrombospondin-1 binding to cAMP reduction, Rac/Cdc42 activation, integrin avidity modulation, and cell migration [PMID:10085089, PMID:11306274, PMID:14966135, PMID:15215311]. CD47 surface levels are transcriptionally controlled by MYC, HIF, and TNF–NF-κB pathways and post-translationally stabilized by EGFR–c-Src phosphorylation at Y288, which blocks TRIM21-mediated ubiquitylation and proteasomal degradation; loss or blockade of CD47 enhances autophagic flux, confers radioprotection, and in the developing brain permits microglial engulfment of synapses in an activity-dependent manner [PMID:26966191, PMID:37541303, PMID:22874555, PMID:30308165].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Establishing that CD47 exists as four alternatively spliced isoforms with tissue-specific expression resolved how a single gene could serve distinct functions in brain, bone marrow, and epithelial compartments.\",\n      \"evidence\": \"PCR, isoform-specific antibodies, and immunohistochemistry on mouse and human tissue panels\",\n      \"pmids\": [\"8586654\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional differences between isoforms remain largely undefined\", \"No structural basis for how cytoplasmic tail variants alter signaling\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Demonstrating that CD47 physically couples to heterotrimeric Gi proteins and β3 integrin in a ternary complex, with thrombospondin-derived peptides stimulating GTPγS binding and cAMP reduction, established CD47 as a bona fide Gi-coupled co-receptor.\",\n      \"evidence\": \"Immunoprecipitation, affinity chromatography, GTPγS binding, cAMP measurement, and pertussis toxin inhibition in platelets and CHO cells\",\n      \"pmids\": [\"10085089\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct structural interface between CD47 multiply-spanning domain and Gαi not resolved\", \"Stoichiometry of the CD47–integrin–Gi complex unknown\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"The finding that anti-CD47 antibodies induce a rapid, Fas/TNF-independent apoptotic pathway in activated T cells revealed a pro-death signaling capacity distinct from its integrin-modulatory function.\",\n      \"evidence\": \"Anti-CD47 mAb (Ad22), annexin V/PI staining, and signaling-deficient Jurkat variant panel\",\n      \"pmids\": [\"10358145\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream death effectors not identified\", \"Single antibody epitope; generalizability to physiological ligands unclear\", \"Not independently replicated in primary T cells at that time\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"The discovery that CD47 knockout red blood cells are rapidly cleared by splenic macrophages established CD47 as a 'marker of self' and defined the foundational concept of a phagocytic checkpoint.\",\n      \"evidence\": \"CD47-knockout mice, in vivo RBC clearance assay, functional phagocytosis measurement\",\n      \"pmids\": [\"10856220\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signaling cascade downstream of SIRPα in macrophages not yet mapped\", \"Whether the checkpoint extends to nucleated cells was untested\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Mapping the CD47–SIRPα interaction to their N-terminal IgV domains and linking it to macrophage fusion provided the structural basis for the inhibitory checkpoint and revealed a role in multinucleated giant cell formation.\",\n      \"evidence\": \"GST-CD47 fusion binding, co-immunoprecipitation, antibody blocking, multinucleation assay\",\n      \"pmids\": [\"10964914\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-resolution structure of the CD47–SIRPα interface not yet available\", \"Signaling events connecting SIRPα engagement to fusion machinery unknown\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showing that CD47 enhances αvβ3 integrin avidity through both cholesterol-independent clustering and cholesterol-dependent raft recruitment, with only the latter enabling Gi signaling, dissected the dual mechanism by which CD47 modulates integrin function.\",\n      \"evidence\": \"LIBS mAb integrin activation reporter, chemical crosslinking, methyl-β-cyclodextrin raft disruption, detergent-free fractionation\",\n      \"pmids\": [\"14966135\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of intermediate signaling molecules between CD47 raft recruitment and Gi activation unknown\", \"Applicability to non-αvβ3 integrins untested at this resolution\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"CD47 overexpression in neurons promoted dendritic outgrowth and upregulated synaptic proteins via MAPK activation, establishing a neuronal signaling role beyond the immune checkpoint function.\",\n      \"evidence\": \"Viral overexpression, siRNA knockdown, MAPK assay, glutamate release and Ca²⁺ imaging in cortical neurons\",\n      \"pmids\": [\"15297459\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which MAPK cascade member is directly activated by CD47 is unresolved\", \"Relevance to in vivo synaptogenesis not yet shown at this point\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identification of BNIP3 as a CD47-binding proapoptotic effector that is stabilized by CD47 and mediates TSP-1-dependent T cell apoptosis provided a molecular mechanism for CD47-driven inflammation resolution.\",\n      \"evidence\": \"CD47-KO and TSP-KO mice, co-immunoprecipitation of CD47–BNIP3, inflammation assays\",\n      \"pmids\": [\"17442977\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of the CD47–BNIP3 interaction not defined\", \"Whether BNIP3 pathway operates in non-T cells expressing CD47 unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstrating that porcine CD47 fails to trigger human SIRPα phosphorylation, while human CD47 expression on porcine cells rescues them from phagocytosis, established species specificity as a barrier in xenotransplantation.\",\n      \"evidence\": \"SIRPα phosphorylation assay, soluble CD47-Fc inhibition, transgenic human CD47 on porcine cells with phagocytosis readout\",\n      \"pmids\": [\"17360380\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Residues determining species specificity not fully mapped\", \"In vivo xenograft survival benefit not quantified long-term\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Consolidating evidence that SIRPα recruits SHP-1/SHP-2 through its cytoplasmic ITIMs upon CD47 ligation unified the phagocytic checkpoint, migration, and neuronal-network regulation under one signaling framework.\",\n      \"evidence\": \"Biochemical binding, phosphorylation studies, functional phagocytosis and migration assays reviewed\",\n      \"pmids\": [\"19144521\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contributions of SHP-1 vs. SHP-2 in different cell types unresolved\", \"Targets dephosphorylated at the phagocytic cup not catalogued\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"The observation that CD47 deficiency or blockade activates autophagic flux and confers radioprotection revealed that CD47 tonically suppresses autophagy, linking the checkpoint receptor to stress resistance.\",\n      \"evidence\": \"CD47-KO mice and cells, electron microscopy of autophagosomes, LC3/BECN1/ATG5/ATG7/p62 quantification, CD47 re-expression rescue\",\n      \"pmids\": [\"22874555\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which CD47 suppresses autophagy initiation unknown\", \"Whether autophagy regulation is SIRPα-dependent or cell-autonomous not distinguished\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"ChIP-validated binding of MYC to the CD47 promoter, with enforced CD47 expression rescuing tumor growth after MYC inactivation, established MYC as a direct transcriptional driver of immune evasion through CD47.\",\n      \"evidence\": \"ChIP, conditional MYC inactivation in mouse tumors, shRNA, flow cytometry, qRT-PCR, enforced CD47 rescue\",\n      \"pmids\": [\"26966191\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether MYC regulation of CD47 operates in non-transformed tissues unknown\", \"Epigenetic co-factors at the CD47 promoter not identified\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identification of a TNF–NF-κB1-responsive constituent enhancer within a breast-cancer-specific CD47 super-enhancer revealed how inflammatory signaling amplifies CD47 transcription in a context-dependent manner.\",\n      \"evidence\": \"ChIP-seq, CRISPR enhancer deletion, luciferase reporter, TNF-α stimulation with NF-κB inhibition\",\n      \"pmids\": [\"28378740\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this super-enhancer operates in non-breast cancer contexts untested\", \"Transcription factor co-occupancy at the super-enhancer not fully mapped\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrating that CD47-deficient mice exhibit excessive microglial engulfment of retinogeniculate synapses and fail to activity-dependently spare active inputs established CD47 as a neuronal 'don't eat me' signal that protects synapses during developmental pruning.\",\n      \"evidence\": \"CD47-KO mice, confocal engulfment imaging, electrophysiology, activity manipulation\",\n      \"pmids\": [\"30308165\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether microglial SIRPα is the cognate receptor in this context was assumed but not directly tested\", \"Mechanism of activity-dependent CD47 regulation on individual synapses unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Quantitative reconstitution showing that macrophage phagocytic decisions depend on a ≥10:1 ratio of activating (FcγR) to inhibitory (SIRPα–CD47) signals, with SIRPα engagement suppressing FcγR phosphorylation, provided a biophysical framework for the checkpoint's signal integration logic.\",\n      \"evidence\": \"Chimeric receptor reconstitution, quantitative ligand density titration, FcγR phosphorylation assay\",\n      \"pmids\": [\"34433055\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this ratio threshold applies in vivo with native receptor densities untested\", \"Contributions of other 'eat me' and 'don't eat me' signals to the ratio not included\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Discovery that NK cells express functional SIRPα that is upregulated by IL-2 and suppressed by CD47 on targets extended the CD47 checkpoint beyond myeloid phagocytes to innate lymphoid cytotoxicity.\",\n      \"evidence\": \"NK cell SIRPα expression analysis, cytotoxicity assays, SIRPα-KO, antibody blockade\",\n      \"pmids\": [\"33416832\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream signaling events in NK cells after SIRPα–CD47 engagement not characterized\", \"Whether this axis operates on all NK cell subsets unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identification of EGFR–c-Src-mediated Y288 phosphorylation that blocks TRIM21-mediated K99/K102 polyubiquitylation and proteasomal degradation of CD47 revealed a post-translational stabilization mechanism exploited by tumors.\",\n      \"evidence\": \"Co-IP, mass spectrometry, Y288F and K99/102R knock-in mutagenesis, ubiquitylation and phagocytosis assays, in vivo brain tumor model\",\n      \"pmids\": [\"37541303\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TRIM21-dependent CD47 degradation operates in non-EGFR-driven cancers unknown\", \"Other kinases that may phosphorylate Y288 not surveyed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrating that SHP2 is constitutively neddylated at K358/K364 to maintain autoinhibition, and that SENP8-mediated deneddylation upon SIRPα engagement activates SHP2 at the phagocytic cup, resolved a missing step in CD47–SIRPα downstream signaling.\",\n      \"evidence\": \"Mass spectrometry neddylation-site mapping, site-directed mutagenesis, SENP8 knockdown, SHP2 activity and phagocytosis assays\",\n      \"pmids\": [\"36626230\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How SIRPα engagement triggers SENP8 recruitment or activation is unknown\", \"Whether SHP1 is similarly regulated by neddylation untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Engineering a CD47 variant (Q31P, '47E') that engages SIRPα but evades therapeutic anti-CD47 antibodies demonstrated that the checkpoint can be harnessed to protect adoptively transferred CAR T cells from macrophage clearance.\",\n      \"evidence\": \"In vivo CAR T cell clearance, CD47 variant engineering, anti-CD47 antibody treatment, multiple tumor models\",\n      \"pmids\": [\"38750365\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Long-term immunological consequences of 47E-expressing T cells in patients unknown\", \"Whether 47E alters thrombospondin-1 binding or Gi signaling untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: the structural basis for how CD47's multiply-spanning transmembrane domain couples to Gi proteins and integrins; the mechanism by which CD47 tonically suppresses autophagy; and how activity-dependent regulation of CD47 at individual synapses is achieved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution structure of full-length CD47 in complex with Gi or integrin\", \"Cell-autonomous vs. SIRPα-dependent signaling not fully dissected for autophagy regulation\", \"Molecular link between neuronal activity and local CD47 surface expression at synapses unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 3, 4, 14, 18]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2, 11]},\n      {\"term_id\": \"GO:0098631\", \"supporting_discovery_ids\": [3, 19]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1, 3, 11, 16]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:R-HSA-168256\", \"supporting_discovery_ids\": [0, 4, 5, 14, 18, 24]},\n      {\"term_id\": \"GO:R-HSA-162582\", \"supporting_discovery_ids\": [2, 4, 10, 17]},\n      {\"term_id\": \"GO:R-HSA-5357801\", \"supporting_discovery_ids\": [8, 9]},\n      {\"term_id\": \"GO:R-HSA-9612973\", \"supporting_discovery_ids\": [13]},\n      {\"term_id\": \"GO:R-HSA-112316\", \"supporting_discovery_ids\": [10, 15]}\n    ],\n    \"complexes\": [\n      \"CD47–SIRPα\",\n      \"CD47–αvβ3 integrin–Gi\"\n    ],\n    \"partners\": [\n      \"SIRPA\",\n      \"ITGB3\",\n      \"THBS1\",\n      \"GNAI2\",\n      \"BNIP3\",\n      \"TRIM21\",\n      \"SRC\",\n      \"SENP8\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}