CD28

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0042102 positive regulation of T cell proliferation	IBA GO_REF:0000033	ACCEPT	Summary: CD28 costimulation is one of the best-characterized drivers of T cell proliferation. Anti-CD28 antibodies costimulate T cell proliferation in conjunction with TCR/CD3 signaling (PMID:3159820). The deep research review confirms CD28 promotes clonal expansion through PI3K/AKT, MAPK, and NF-kB/AP-1/NFAT programmes. Reason: Positive regulation of T cell proliferation is a core function of CD28. This IBA annotation is well supported by extensive experimental literature showing CD28 costimulation is essential for T cell proliferation. The term is at an appropriate level of specificity. Supporting Evidence: PMID:3159820 mAb 9.3 was capable of inducing T cell proliferation in the presence of 12-o-tetradecanoyl phorbol-13-acetate (TPA) file:human/CD28/CD28-deep-research-falcon.md CD28 is the prototypic co‑stimulatory receptor (signal 2) that integrates with TCR signalling (signal 1) to enable full T cell activation. It stabilizes IL‑2 transcription and mRNA, promotes survival (e.g., Bcl‑xL upregulation), and drives clonal expansion
GO:0042110 T cell activation	IBA GO_REF:0000033	ACCEPT	Summary: T cell activation is the central biological process in which CD28 participates. The deep research review identifies CD28 as the prototypic costimulatory receptor providing signal 2 for T cell activation. UniProt describes CD28 as a receptor that plays a role in T-cell activation. Reason: T cell activation is a core function of CD28. The IBA annotation is consistent with the primary biological role of this receptor. Supported by extensive literature and phylogenetic conservation. Supporting Evidence: PMID:1650475 B-cell surface antigen B7 provides a costimulatory signal that induces T cells to proliferate and secrete interleukin 2 file:human/CD28/CD28-deep-research-falcon.md CD28 is the prototypic co-stimulatory receptor (signal 2) that integrates with TCR signalling (signal 1) to enable full T cell activation
GO:0009897 external side of plasma membrane	IBA GO_REF:0000033	ACCEPT	Summary: CD28 is a type I transmembrane protein with its IgV-type ligand-binding domain on the external side of the plasma membrane. UniProt annotation confirms extracellular domain spanning residues 19-152. IDA evidence from PMID:11390434 directly demonstrates cell surface expression. Reason: External side of plasma membrane is the correct localization for CD28's functional domain. The extracellular IgV domain binds B7 ligands (CD80/CD86) and this is where CD28 carries out its receptor function. Phylogenetically conserved localization. Supporting Evidence: PMID:11390434 the following Abs (all IgM) were used: CD4 (MEM-16), CD5 (MEM-128), and CD28 (248.23.2; reference 25) file:human/CD28/CD28-uniprot.txt TOPO_DOM 19..152 /note=Extracellular
GO:0031295 T cell costimulation	IBA GO_REF:0000033	ACCEPT	Summary: T cell costimulation is the defining biological process for CD28. It provides the critical signal 2 that cooperates with TCR engagement to enable full T cell activation and prevent anergy. This is the most precise BP term for CD28's role. Reason: T cell costimulation is the single most accurate biological process term for CD28 and represents its core function. CD28 is literally the prototypic T cell costimulatory receptor. Strongly supported by IBA phylogenetic evidence and extensive literature. Supporting Evidence: PMID:8617933 ligation of CD3/TCR and CD28 in the absence of CD40L triggering resulted in little or no IL-4 synthesis file:human/CD28/CD28-deep-research-falcon.md CD28 is the prototypic co-stimulatory receptor (signal 2)
GO:0050852 T cell receptor signaling pathway	IBA GO_REF:0000033	ACCEPT	Summary: CD28 costimulation amplifies and modulates TCR signaling. The 2024 imaging study demonstrates that CD28 costimulation specifically accelerates Lck recruitment and ZAP70 activation within TCR microclusters. CD28 delivers unique signals that alter the gene expression program of T cells beyond simple TCR amplification (PMID:24665965 per UniProt). Reason: CD28 is intimately coupled to the TCR signaling pathway - it amplifies proximal TCR signals by recruiting Lck to TCR microclusters, lowers the activation threshold, and feeds into the same downstream NF-kB/NFAT/AP-1 transcriptional programs. The IBA annotation is phylogenetically sound and well supported. Supporting Evidence: file:human/CD28/CD28-deep-research-falcon.md CD28 co-stimulation accelerates recruitment of Lck into TCR microclusters, which in turn accelerates ZAP70 recruitment and activation, effectively lowering the TCR activation threshold
GO:0002376 immune system process	IEA GO_REF:0000117	ACCEPT	Summary: Immune system process is a very broad parent term. CD28 is clearly involved in immune system processes as the primary T cell costimulatory receptor. However, this is much less informative than the more specific terms already annotated (T cell costimulation, T cell activation, etc.). Reason: While very broad, this IEA annotation is not incorrect. CD28 is fundamentally an immune system molecule. More specific child terms are already present. Acceptable as a broad IEA mapping.
GO:0005886 plasma membrane	IEA GO_REF:0000044	ACCEPT	Summary: CD28 is a type I single-pass transmembrane protein that localizes to the plasma membrane. UniProt subcellular location annotation confirms cell membrane localization. Multiple IDA annotations also support this. Reason: Plasma membrane is the correct localization for CD28. This IEA annotation is consistent with multiple higher-evidence annotations (IDA) for the same term. Well supported by UniProt subcellular location.
GO:0006955 immune response	IEA GO_REF:0000002	ACCEPT	Summary: Immune response is a broad BP term from InterPro mapping based on the CD28 domain (IPR008093). CD28 is essential for adaptive immune responses, particularly T cell-mediated immunity. Reason: While broad, the IEA annotation from InterPro mapping is correct. CD28 is a central player in adaptive immune responses. More specific terms (T cell costimulation, T cell activation) provide the needed detail.
GO:0009986 cell surface	IEA GO_REF:0000044	ACCEPT	Summary: Cell surface localization is correct for CD28, which is expressed on the T cell surface. Also supported by IDA evidence from PMID:15067037. Reason: Correct IEA annotation. CD28 is a cell surface receptor. Consistent with IDA evidence from PMID:15067037 and the external side of plasma membrane IBA annotation.
GO:0016020 membrane	IEA GO_REF:0000002	ACCEPT	Summary: Membrane is a very broad CC term from InterPro mapping. CD28 is a transmembrane protein, so this is correct but uninformative given more specific terms (plasma membrane, external side of plasma membrane). Reason: Correct but very broad. More specific CC annotations are available. Acceptable as a broad IEA mapping from InterPro.
GO:0042129 regulation of T cell proliferation	IEA GO_REF:0000002	ACCEPT	Summary: Regulation of T cell proliferation from InterPro mapping (IPR040216 CTLA4/CD28 domain). CD28 positively regulates T cell proliferation, so this parent term is correct. Reason: Correct IEA annotation. The more specific child term GO:0042102 (positive regulation of T cell proliferation) is also annotated with experimental evidence. This broader IEA term is acceptable.
GO:0050870 positive regulation of T cell activation	IEA GO_REF:0000117	ACCEPT	Summary: Positive regulation of T cell activation is appropriate for CD28. CD28 costimulation positively regulates T cell activation by lowering the TCR activation threshold, promoting cytokine production, and driving proliferation. Reason: Correct IEA annotation. CD28 is the canonical positive regulator of T cell activation. Consistent with the IBA annotation for T cell activation and the experimental evidence for costimulation.
GO:0005515 protein binding	IPI PMID:10820259 GRID: a novel Grb-2-related adapter protein that interacts w...	MODIFY	Summary: IPI annotation for protein binding based on interaction with PIK3R1 (P27986, the p85 regulatory subunit of PI3K). The CD28 YMNM motif recruits PI3K via the p85 SH2 domain. This is a functionally important interaction for CD28 signaling. Reason: Protein binding is uninformative. The interaction with PIK3R1 (p85) is a well-characterized signaling interaction via the YMNM motif. This should be captured with a more specific MF term reflecting the signaling adaptor recruitment function. Proposed replacements: protein kinase binding Supporting Evidence: PMID:7568038 p56Lck and p59Fyn regulate CD28 binding to phosphatidylinositol 3-kinase, growth factor receptor-bound protein GRB-2, and T cell-specific protein-tyrosine kinase ITK
GO:0005515 protein binding	IPI PMID:18641334 ICOS ligation recruits the p50alpha PI3K regulatory subunit ...	MODIFY	Summary: IPI annotation for protein binding based on interaction with PIK3R1 (P27986). Another publication documenting CD28-PI3K p85 interaction. Publication not available for review. Reason: Protein binding is uninformative. Same as above - should be protein kinase binding or a more specific term reflecting CD28-PI3K signaling interaction. Proposed replacements: protein kinase binding
GO:0005515 protein binding	IPI PMID:21982860 A secreted protein microarray platform for extracellular pro...	MODIFY	Summary: High-throughput secreted protein microarray screen identifying CD28 interaction with CD80 (P33681/B7-1). This is a core ligand-receptor interaction. The paper describes a screening platform for extracellular protein interaction discovery. Reason: Protein binding is uninformative for the CD28-CD80 ligand-receptor interaction. CD28 binding to CD80 is the fundamental receptor-ligand interaction that defines CD28 function. The coreceptor activity term (GO:0015026) already captures this MF more precisely. Proposed replacements: coreceptor activity Supporting Evidence: PMID:21982860 functional protein microarrays are particularly well-suited for high-throughput screening of extracellular protein interactions
GO:0005515 protein binding	IPI PMID:32822567 A Human IgSF Cell-Surface Interactome Reveals a Complex Netw...	MODIFY	Summary: IgSF cell-surface interactome study confirming CD28 interaction with CD80 (P33681). This large-scale study systematically mapped direct protein interactions across a recombinant IgSF library. Reason: Protein binding is too vague for CD28-CD80 receptor-ligand interaction. This is a core functional interaction already captured by coreceptor activity. Proposed replacements: coreceptor activity Supporting Evidence: PMID:32822567 Cell-surface protein-protein interactions (PPIs) mediate cell-cell communication, recognition, and responses
GO:0005515 protein binding	IPI PMID:32822567 A Human IgSF Cell-Surface Interactome Reveals a Complex Netw...	MODIFY	Summary: Same IgSF interactome study, this entry for CD28 interaction with CD86 (P42081/B7-2). CD86 is the other principal ligand for CD28 alongside CD80. Reason: Protein binding is uninformative. CD28-CD86 is a core receptor-ligand interaction. Should be captured under coreceptor activity. Proposed replacements: coreceptor activity
GO:0005515 protein binding	IPI PMID:35922511 A physical wiring diagram for the human immune system.	MODIFY	Summary: Physical wiring diagram for the human immune system confirming CD28-CD80 interaction. Large-scale systematic mapping of direct protein interactions across human leukocyte surface proteins. Reason: Protein binding is uninformative. Another confirmation of the CD28-CD80 core ligand interaction. Should be coreceptor activity. Proposed replacements: coreceptor activity Supporting Evidence: PMID:35922511 using a high-throughput surface receptor screening method, we systematically mapped the direct protein interactions across a recombinant library that encompasses most of the surface proteins that are detectable on human leukocytes
GO:0005515 protein binding	IPI PMID:35922511 A physical wiring diagram for the human immune system.	MODIFY	Summary: Same wiring diagram study, this entry for CD28-CD86 (P42081) interaction. Reason: Protein binding is uninformative for CD28-CD86 core ligand interaction. Should be coreceptor activity. Proposed replacements: coreceptor activity
GO:0005515 protein binding	IPI PMID:7568038 p56Lck and p59Fyn regulate CD28 binding to phosphatidylinosi...	MODIFY	Summary: Raab et al. 1995 demonstrated that Lck and Fyn regulate CD28 binding to PI3K (PIK3R1/p85), GRB2, and ITK. Mutation of Tyr-191 greatly reduced phosphorylation by Lck. The with/from column indicates PIK3R1 (P27986). This paper is a foundational study of CD28 signaling. Reason: Protein binding is uninformative for this well-characterized signaling interaction. CD28-PI3K interaction is mediated by the YMNM motif and is critical for costimulatory signaling. Should be protein kinase binding. Proposed replacements: protein kinase binding Supporting Evidence: PMID:7568038 p56Lck and p59Fyn regulate CD28 binding to phosphatidylinositol 3-kinase, growth factor receptor-bound protein GRB-2, and T cell-specific protein-tyrosine kinase ITK
GO:0005515 protein binding	IPI PMID:7584133 Selective CD28pYMNM mutations implicate phosphatidylinositol...	MODIFY	Summary: Cai et al. 1995 showed that CD28 pYMNM mutations disrupt PI3K and GRB2 binding, directly implicating PI3K in CD28-mediated costimulation leading to IL-2 secretion. With/from indicates PIK3R1 (P27986). Reason: Protein binding is uninformative. This foundational paper demonstrates that the CD28-PI3K interaction via the YMNM motif is essential for costimulation. Should be protein kinase binding. Proposed replacements: protein kinase binding Supporting Evidence: PMID:7584133 Both Y191CD28F and M194CD28C mutants failed to generate IL-2. These data directly implicate PI 3-kinase in CD28-mediated costimulation leading to IL-2 secretion
GO:0005515 protein binding	IPI PMID:7807015 CTLA-4 binding to the lipid kinase phosphatidylinositol 3-ki...	MODIFY	Summary: Schneider et al. 1995 studied CTLA-4 binding to PI3K, but with/from indicates PIK3R1 (P27986). The paper demonstrates that CTLA-4 also associates with PI3K, comparing binding affinities with CD28. CD28 data was used as a reference point. Reason: Protein binding is uninformative. This documents the CD28-PI3K p85 interaction in comparison to CTLA-4. Should be protein kinase binding. Proposed replacements: protein kinase binding Supporting Evidence: PMID:7807015 the NH2- and COOH-terminal SH2 domains of p85 bind the CTLA-4 cytoplasmic pYVKM motif with an affinity (ID50: 0.6 and 0.04 microM), that is similar to CD28
GO:0005515 protein binding	IPI PMID:8146197 T-cell antigen CD28 interacts with the lipid kinase phosphat...	MODIFY	Summary: Publication not available for review. With/from indicates PIK3R1 (P27986). Likely another study documenting the CD28-PI3K p85 interaction. Reason: Protein binding is uninformative. Based on the with/from column indicating PIK3R1 interaction, should be protein kinase binding. Publication not available to confirm specific details. Proposed replacements: protein kinase binding
GO:0005515 protein binding	IPI PMID:8183372 Binding of phosphatidylinositol-3-OH kinase to CD28 is requi...	MODIFY	Summary: Publication not available for review. With/from indicates PIK3R1 (P27986). Another study documenting CD28-PI3K interaction. Reason: Protein binding is uninformative. Based on with/from indicating PIK3R1, should be protein kinase binding. Publication not available. Proposed replacements: protein kinase binding
GO:0005515 protein binding	IPI PMID:9417079 Growth factor receptor-bound protein 2 SH2/SH3 domain bindin...	MODIFY	Summary: Kim et al. 1998 characterized GRB2 SH2/SH3 domain binding to CD28 and its role in co-signaling. Both SH2 and SH3 domains contribute to CD28 binding. Mutations that alter GRB2 binding blocked CD28-dependent IL-2 production and Vav phosphorylation. With/from indicates PIK3R1 (P27986). Reason: Protein binding is uninformative. This paper documents functional significance of GRB2 binding to CD28 via both SH2 and SH3 domains. Should be more specific. Proposed replacements: protein kinase binding Supporting Evidence: PMID:9417079 Mutations that alter Grb2 binding were found to block the CD28-dependent interleukin-2 production. Further, tyrosine phosphorylation of Vav and the costimulation-dependent activation of Jun N-terminal kinase was blocked
GO:0001772 immunological synapse	IEA GO_REF:0000107	ACCEPT	Summary: Ensembl Compara transfer from mouse CD28 (P31041). CD28 localizes to the immunological synapse upon T cell-APC contact, where it co-assembles with TCR microclusters. The 2024 TIRF microscopy study directly demonstrates CD28 costimulation shapes signaling within TCR microclusters at the immune synapse. Reason: Immunological synapse localization is well established for CD28. This is where CD28 carries out its costimulatory function by recruiting Lck to TCR microclusters. The IEA transfer from mouse is consistent with extensive experimental evidence. Supporting Evidence: file:human/CD28/CD28-deep-research-falcon.md CD28 co-localizes with TCR microclusters within the immune synapse
GO:0009897 external side of plasma membrane	IEA GO_REF:0000107	ACCEPT	Summary: Ensembl Compara transfer from mouse CD28. Consistent with IBA annotation for same term and IDA evidence from PMID:11390434. Reason: Correct IEA annotation. Consistent with IBA and IDA evidence for the same term.
GO:0019901 protein kinase binding	IEA GO_REF:0000107	ACCEPT	Summary: Ensembl Compara transfer from mouse. CD28 binds multiple protein kinases including PI3K (via p85 regulatory subunit, YMNM motif), Lck (via PYAP motif), ITK (via PRRP motif), and PKC-theta. This is a well-documented core molecular function. Reason: Protein kinase binding is well supported for CD28. The cytoplasmic tail recruits PI3K, Lck, ITK, and PKC-theta through distinct motifs. This IEA is consistent with extensive experimental evidence and is a far more informative MF term than generic protein binding. Supporting Evidence: PMID:7568038 p56Lck and p59Fyn regulate CD28 binding to phosphatidylinositol 3-kinase, growth factor receptor-bound protein GRB-2, and T cell-specific protein-tyrosine kinase ITK file:human/CD28/CD28-deep-research-falcon.md YMNM (binds PI3K and GRB2), PRRP (recruits ITK leading to PLCgamma1 and SLP-76/GADS engagement), and PYAP (dominant for LCK binding and assembly of PKCtheta at the synapse)
GO:0005886 plasma membrane	IDA GO_REF:0000052	ACCEPT	Summary: IDA annotation based on immunofluorescence data (HPA). CD28 is a transmembrane protein at the plasma membrane. Reason: Plasma membrane localization is unambiguously correct for CD28. Supported by immunofluorescence and consistent with the known type I transmembrane topology.
GO:0004888 transmembrane signaling receptor activity	IDA PMID:11279501 Structural basis for co-stimulation by the human CTLA-4/B7-2...	ACCEPT	Summary: Schwartz et al. 2001 solved the crystal structure of the CTLA-4/B7-2 complex, providing structural basis for costimulation. The paper discusses both CD28 and CTLA-4 as transmembrane signaling receptors that engage B7 ligands. CD28 ligation with B7 ligands initiates intracellular signaling cascades. Reason: Transmembrane signaling receptor activity is an appropriate MF for CD28. CD28 spans the membrane and upon ligand (CD80/CD86) binding, transmits signals intracellularly through its cytoplasmic YMNM/PRRP/PYAP motifs. This term is accurate but somewhat general; coreceptor activity (GO:0015026) is more precise. Supporting Evidence: PMID:11279501 Regulation of T-cell activity is dependent on antigen-independent co-stimulatory signals provided by the disulphide-linked homodimeric T-cell surface receptors, CD28 and CTLA-4
GO:0004888 transmembrane signaling receptor activity	IDA PMID:12196291 The interaction properties of costimulatory molecules revisi...	ACCEPT	Summary: Collins et al. 2002 revisited the interaction properties of costimulatory molecules including CD28 with CD80 and CD86. UniProt cites this paper for CD28 function and interaction with CD80/CD86. Publication not available but UniProt annotates it for CD28 function. Reason: Transmembrane signaling receptor activity is correct for CD28. This paper provided key interaction data for CD28-B7 engagement.
GO:0005886 plasma membrane	IDA PMID:35397202 Structural characterization of a dimerization interface in t...	ACCEPT	Summary: Wu et al. 2022 characterized the dimerization interface in the CD28 transmembrane domain by NMR. UniProt cites this for subcellular location (cell membrane). The paper confirms CD28 as a membrane protein and characterizes TM helix dimerization. Reason: IDA evidence directly confirming plasma membrane localization via structural characterization of the transmembrane domain. Supporting Evidence: file:human/CD28/CD28-uniprot.txt SUBCELLULAR LOCATION: Cell membrane {ECO:0000269\|PubMed:35397202}; Single-pass type I membrane protein
GO:0050862 positive regulation of T cell receptor signaling pathway	IDA PMID:11279501 Structural basis for co-stimulation by the human CTLA-4/B7-2...	ACCEPT	Summary: Schwartz et al. 2001 structural study of CTLA-4/B7-2 complex. The paper demonstrates that CD28 engagement with B7 ligands provides a stimulatory signal for T cell activation, consistent with positive regulation of TCR signaling. Reason: Positive regulation of TCR signaling pathway is a core function of CD28. CD28 costimulation amplifies TCR signals by recruiting Lck to TCR microclusters and lowering activation thresholds. Well supported by this and many other studies. Supporting Evidence: PMID:11279501 Engagement of CD28 with B7-1 and B7-2 ligands on antigen-presenting cells (APCs) provides a stimulatory signal for T-cell activation
GO:0050862 positive regulation of T cell receptor signaling pathway	IDA PMID:12196291 The interaction properties of costimulatory molecules revisi...	ACCEPT	Summary: Collins et al. 2002 characterized interaction properties of costimulatory molecules. UniProt cites this for CD28's function in increasing proliferation and cytokine expression. Reason: Same core function. Multiple IDA annotations for positive regulation of TCR signaling from different publications strengthens the evidence. Consistent with CD28's role as the prototypic TCR costimulatory receptor.
GO:0050862 positive regulation of T cell receptor signaling pathway	IDA PMID:1650475 B-cell surface antigen B7 provides a costimulatory signal th...	ACCEPT	Summary: Gimmi et al. 1991, a foundational paper showing B7 provides a costimulatory signal that induces T cells to proliferate and secrete IL-2. UniProt cites this for CD28 function. Publication not available but this is one of the original demonstrations of CD28/B7 costimulation. Reason: This is one of the earliest and most important studies demonstrating that B7-CD28 costimulation positively regulates T cell responses. Core annotation well supported by this seminal publication.
GO:0004888 transmembrane signaling receptor activity	TAS PMID:9784967 CD28/B7 costimulation: a review.	ACCEPT	Summary: TAS annotation based on a review. CD28 is clearly a transmembrane signaling receptor. Publication not available for review. Reason: Transmembrane signaling receptor activity is correct. CD28 is a type I transmembrane receptor that signals upon ligand engagement. TAS annotation is appropriate for a review-based citation.
GO:0042110 T cell activation	IDA PMID:23918985 Soluble CD80 restores T cell activation and overcomes tumor ...	ACCEPT	Summary: IDA annotation for T cell activation. Publication not available for review. UniProt cites CD28's role in T cell activation from multiple publications. Reason: T cell activation is a core function of CD28. While the specific publication is not available, this annotation is consistent with the overwhelming body of evidence for CD28 in T cell activation.
GO:0042110 T cell activation	IGI PMID:18337562 CCL5-mediated T-cell chemotaxis involves the initiation of m...	ACCEPT	Summary: IGI annotation for T cell activation with genetic interactor IL-4 (P05112). The referenced publication PMID:18337562 (Murooka et al. 2008) focuses on CCL5-mediated T cell chemotaxis and mTOR signaling, not directly on CD28. However, T cell activation is the defining biological process for CD28, supported by overwhelming evidence from multiple other publications and the IBA and IDA annotations for the same term. CD28 is the prototypic T cell costimulatory receptor; its role in T cell activation is beyond question (PMID:1650475, PMID:23918985, PMID:11279501). Reason: Although the specific publication (PMID:18337562) is about CCL5-mediated chemotaxis rather than CD28 per se, T cell activation is the single most well-established function of CD28. The IBA and IDA annotations for this same term are already accepted. CD28 is literally defined as the prototypic T cell costimulatory receptor, and T cell activation is its core function. The IGI evidence code with IL-4 as genetic interactor is consistent with the known role of CD28 costimulation in cytokine-dependent T cell activation programs. Resolving to ACCEPT for consistency with the other GO:0042110 annotations. Supporting Evidence: PMID:1650475 B7-transfected CHO cells can induce suboptimally activated CD28+ T cells to proliferate and secrete high levels of interleukin 2 PMID:11279501 Engagement of CD28 with B7-1 and B7-2 ligands on antigen-presenting cells (APCs) provides a stimulatory signal for T-cell activation file:human/CD28/CD28-deep-research-falcon.md CD28 is the prototypic co-stimulatory receptor (signal 2) that integrates with TCR signalling (signal 1) to enable full T cell activation
GO:0010628 positive regulation of gene expression	IMP PMID:23817958 Proinflammatory stimuli induce galectin-9 in human mesenchym...	KEEP AS NON CORE	Summary: IMP annotation for positive regulation of gene expression. Publication not available. CD28 signaling is known to activate NF-kB, NFAT, and AP-1 transcription factors, which positively regulate expression of many target genes including IL-2. Reason: While CD28 signaling does regulate gene expression programs through NF-kB/NFAT/AP-1 activation, this is a very broad downstream effect rather than a core molecular function of CD28 itself. The annotation is not wrong, but represents a downstream consequence of CD28 costimulatory signaling rather than a defining function. Publication not available to assess specific experimental context.
GO:0010629 negative regulation of gene expression	IMP PMID:23817958 Proinflammatory stimuli induce galectin-9 in human mesenchym...	KEEP AS NON CORE	Summary: IMP annotation for negative regulation of gene expression from the same publication as the positive regulation annotation above. CD28 signaling can indeed both upregulate and downregulate different gene sets. Reason: Same reasoning as for positive regulation of gene expression. This is a downstream consequence of CD28 signaling, not a core function. The annotation may be valid for specific gene sets that are downregulated by CD28 costimulation, but it is a very broad and non-specific annotation. Publication not available.
GO:0043066 negative regulation of apoptotic process	TAS PMID:8717514 CD28/B7 system of T cell costimulation.	KEEP AS NON CORE	Summary: TAS annotation for negative regulation of apoptosis. CD28 signaling promotes T cell survival through upregulation of anti-apoptotic proteins including Bcl-xL. This is a well-known downstream effect of CD28 costimulation. Publication not available. Reason: CD28 signaling does promote cell survival and inhibit apoptosis (e.g., via Bcl-xL upregulation), but this is a downstream consequence of its costimulatory signaling rather than its primary molecular function. It is a pleiotropic effect of CD28 activation, not its defining function. Supporting Evidence: file:human/CD28/CD28-deep-research-falcon.md promotes survival (e.g., Bcl-xL upregulation)
GO:0098636 protein complex involved in cell adhesion	IDA PMID:7544393 Identification of residues in the V domain of CD80 (B7-1) im...	KEEP AS NON CORE	Summary: Fargeas et al. 1995 identified residues in the CD80 V domain implicated in functional interactions with CD28 and CTLA-4. The paper studied CD80-CD28 adhesion and IL-2 production using CD80 mutants. The annotation refers to CD28 as part of a protein complex involved in cell adhesion (T cell-APC interaction). Reason: While CD28-CD80 interaction does contribute to T cell-APC adhesion at the immune synapse, this is not the primary function of CD28. CD28 is fundamentally a signaling coreceptor, not primarily an adhesion molecule. The cell adhesion aspect is secondary to its costimulatory signaling role. Supporting Evidence: PMID:7544393 human CD80 mutants were generated and tested for their ability to maintain the interaction with CD28 leading to adhesion and enhanced IL-2 production
GO:0031295 T cell costimulation	TAS PMID:8617933 Cross-linking of the CD40 ligand on human CD4+ T lymphocytes...	ACCEPT	Summary: Blotta et al. 1996 showed that CD40L costimulation enhances IL-4 synthesis in conjunction with CD3/TCR and CD28 ligation. The paper directly demonstrates CD28's role in T cell costimulation. Reason: T cell costimulation is the core function of CD28. This TAS annotation from a study directly examining CD28 costimulation in conjunction with CD3 and CD40L is well supported. Supporting Evidence: PMID:8617933 IL-4 synthesis was greatly enhanced by triggering of CD40L on the T cell surface in conjunction with ligation of CD3/TCR and CD28
GO:0032733 positive regulation of interleukin-10 production	IDA PMID:8617933 Cross-linking of the CD40 ligand on human CD4+ T lymphocytes...	KEEP AS NON CORE	Summary: Blotta et al. 1996 showed that CD3/CD28/CD40L costimulation enhances cytokine production including IL-10 in T cells. Reason: IL-10 production is a downstream consequence of CD28 costimulation combined with CD40L signaling. While experimentally demonstrated (IDA), this is a specific cytokine output rather than a core function of CD28. The core function is T cell costimulation broadly. Supporting Evidence: PMID:8617933 IL-4 synthesis was greatly enhanced by triggering of CD40L on the T cell surface in conjunction with ligation of CD3/TCR and CD28
GO:0032753 positive regulation of interleukin-4 production	IDA PMID:8617933 Cross-linking of the CD40 ligand on human CD4+ T lymphocytes...	KEEP AS NON CORE	Summary: Blotta et al. 1996 directly demonstrated that CD28 costimulation (with CD3 and CD40L) greatly enhances IL-4 synthesis. This was the main finding of the paper. Reason: IL-4 production enhancement is a specific downstream effect of CD28 costimulation, particularly in combination with CD40L signaling. While experimentally validated, this represents a specific cytokine output rather than the core costimulatory function. Supporting Evidence: PMID:8617933 IL-4 synthesis was greatly enhanced by triggering of CD40L on the T cell surface in conjunction with ligation of CD3/TCR and CD28, whereas ligation of CD3/TCR and CD28 in the absence of CD40L triggering resulted in little or no IL-4 synthesis
GO:0042102 positive regulation of T cell proliferation	IDA PMID:8617933 Cross-linking of the CD40 ligand on human CD4+ T lymphocytes...	ACCEPT	Summary: Blotta et al. 1996 demonstrated T cell proliferation in response to CD3/CD28 costimulation. The paper used anti-CD28 antibodies as costimulatory signals. Reason: Positive regulation of T cell proliferation is a core function of CD28. IDA evidence from Blotta et al. directly demonstrates this. Consistent with multiple other annotations. Supporting Evidence: PMID:8617933 using immobilized mAbs against several T cell surface molecules, including CD3, CD28, and the CD40 ligand (CD40L)
GO:0005515 protein binding	IPI PMID:15067037 The modulation of CD40 ligand signaling by transmembrane CD2...	UNDECIDED	Summary: Mikolajczak et al. 2004 showed that isoform 3 (CD28i) interacts with CD40LG (P29965/CD154). This is an interaction specific to the CD28i splice variant that lacks most of the extracellular domain. Reason: This interaction is specific to isoform 3 (CD28i), which has a truncated extracellular domain and interacts with CD40LG rather than B7 ligands. While the interaction is experimentally demonstrated, it is isoform-specific. Protein binding is uninformative but the isoform-specific nature makes it harder to propose a simple replacement. Supporting Evidence: file:human/CD28/CD28-uniprot.txt Isoform 3: Enhances CD40L-mediated activation of NF-kappa-B and kinases MAPK8 and PAK2 in T-cells
GO:0009986 cell surface	IDA PMID:15067037 The modulation of CD40 ligand signaling by transmembrane CD2...	ACCEPT	Summary: Mikolajczak et al. 2004 demonstrated cell surface localization of isoform 3 (CD28i). UniProt confirms subcellular location for isoform 3 as cell surface. Reason: Cell surface localization is correct for CD28, including isoform 3. IDA evidence directly demonstrates this. Supporting Evidence: file:human/CD28/CD28-uniprot.txt SUBCELLULAR LOCATION: [Isoform 3]: Cell surface
GO:0005886 plasma membrane	TAS Reactome:R-HSA-2316434	ACCEPT	Summary: Reactome annotation for PI3K phosphorylation of PIP2 to PIP3 in context of CD28 signaling at the plasma membrane. Reason: Plasma membrane localization in the context of PI3K signaling downstream of CD28 is correct. CD28 recruits PI3K to the plasma membrane.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-2400009	ACCEPT	Summary: Reactome annotation for PI3K inhibitors blocking PI3K catalytic activity. CD28 at the plasma membrane. Reason: Correct. CD28 at the plasma membrane in PI3K signaling context.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-388814	ACCEPT	Summary: Reactome annotation for Grb2 binding to CD28 at the plasma membrane. Reason: Correct. CD28 recruits Grb2 at the plasma membrane via the YMNM motif.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-388831	ACCEPT	Summary: Reactome annotation for phosphorylation of CD28 at the plasma membrane. Reason: Correct. CD28 is phosphorylated by Lck at the plasma membrane.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-388832	ACCEPT	Summary: Reactome annotation for PI3K binding to CD28 at the plasma membrane. Reason: Correct. PI3K binds CD28 at the plasma membrane via the pYMNM motif.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-389158	ACCEPT	Summary: Reactome annotation for CD28-bound PI3K phosphorylating PIP2 to PIP3. Reason: Correct. PI3K recruited to CD28 at the plasma membrane generates PIP3.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-389348	ACCEPT	Summary: Reactome annotation for activation of Rac1 by pVav1 in the CD28 pathway at the plasma membrane. Reason: Correct. Vav1 activation downstream of CD28 at the plasma membrane leads to Rac1 activation.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-389350	ACCEPT	Summary: Reactome annotation for activation of Cdc42 by pVav1 in the CD28 pathway at the plasma membrane. Reason: Correct. Vav1 activation downstream of CD28 at the plasma membrane leads to Cdc42 activation.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-389352	ACCEPT	Summary: Reactome annotation for translocation of Vav1 to CD28 at the plasma membrane. Reason: Correct. Vav1 is recruited to CD28 at the plasma membrane.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-389354	ACCEPT	Summary: Reactome annotation for activation of Vav1 in the CD28 pathway at the plasma membrane. Reason: Correct. Vav1 is activated in the CD28 signaling pathway at the plasma membrane.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-389381	ACCEPT	Summary: Reactome annotation for Gads binding to CD28 at the plasma membrane. Reason: Correct. Gads is recruited to CD28 at the plasma membrane.
GO:0005829 cytosol	TAS Reactome:R-HSA-167637	KEEP AS NON CORE	Summary: Reactome annotation for internalization of Nef:CD28:Clathrin-Coated Pit Adapter Protein complex. This is in the context of HIV Nef-mediated downregulation of CD28, where CD28 is internalized to the cytosol. Reason: Cytosol localization of CD28 is specific to the HIV Nef-mediated downregulation pathway where CD28 is internalized from the cell surface. This is not a normal physiological localization of CD28 but rather a pathological consequence of viral hijacking. Not a core localization.
GO:0005886 plasma membrane	IDA PMID:11390434 The transmembrane adaptor protein TRIM regulates T cell rece...	ACCEPT	Summary: Kirchgessner et al. 2001 studied the transmembrane adaptor protein TRIM and its association with TCR. CD28 plasma membrane expression was confirmed as part of the characterization of T cell surface molecules. Reason: IDA evidence for plasma membrane localization. Correct and consistent with all other evidence.
GO:0009897 external side of plasma membrane	IDA PMID:11390434 The transmembrane adaptor protein TRIM regulates T cell rece...	ACCEPT	Summary: Same study as above. IDA evidence for external side of plasma membrane localization, consistent with IBA annotation. Reason: IDA evidence confirming CD28's extracellular domain is on the external side of the plasma membrane. Consistent with IBA and IEA annotations for the same term.
GO:0045066 regulatory T cell differentiation	IDA PMID:18641304 Acquisition of suppressive function by activated human CD4+ ...	KEEP AS NON CORE	Summary: Zheng et al. 2008 studied acquisition of suppressive function by activated human CD4+CD25- T cells. The paper focuses on CTLA-4 and FoxP3 in Treg induction, with CD28 involved in the activation that generates these cells. CD28 signaling is required for the initial T cell activation that leads to CTLA-4 upregulation and Treg differentiation. Reason: While CD28 signaling contributes to T cell activation that can lead to Treg differentiation, this paper primarily focuses on CTLA-4 and FoxP3 as the key determinants of regulatory T cell function. CD28's role is in providing the initial activation signal, not specifically in directing the Treg differentiation program. This is a downstream consequence rather than a core function. Supporting Evidence: PMID:18641304 Activation of human CD4(+)CD25(-) T cells resulted in the appearance of a de novo population of FoxP3-expressing cells within 48 h. These cells expressed high levels of CTLA-4
GO:0005886 plasma membrane	TAS Reactome:R-HSA-167630	ACCEPT	Summary: Reactome annotation for Formation of Nef-CD28 cytoplasmic tail complex at the plasma membrane (HIV Nef pathway). Reason: CD28 is at the plasma membrane when Nef interacts with its cytoplasmic tail. Correct localization even in this pathological context.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-167633	ACCEPT	Summary: Reactome annotation for Formation of Nef:CD28:Clathrin-Coated Pit Adapter Protein complex at the plasma membrane. Reason: Correct. CD28 at the plasma membrane in HIV Nef pathway.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-167637	ACCEPT	Summary: Reactome annotation for internalization of the Nef:CD28:Clathrin complex from the plasma membrane. Reason: Correct. CD28 starts at the plasma membrane before Nef-mediated internalization.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-388808	ACCEPT	Summary: Reactome annotation for CD28 homodimer binding B7-2 monomer at the plasma membrane. Reason: Correct. CD28-CD86 interaction occurs at the plasma membrane.
GO:0005886 plasma membrane	TAS Reactome:R-HSA-388811	ACCEPT	Summary: Reactome annotation for CD28 homodimer binding B7-1 homodimer at the plasma membrane. Reason: Correct. CD28-CD80 interaction occurs at the plasma membrane.
GO:0005515 protein binding	IPI PMID:15554700 Characterization of Lck-binding elements in the herpesviral ...	UNDECIDED	Summary: Bauer et al. 2004 characterized Lck-binding elements in the herpesviral Tip protein. The with/from column indicates Lck (P06239). This paper is about viral Tip protein interaction with Lck, not directly about CD28. CD28 may have been used as a reference or control for Lck binding. Reason: The paper is about herpesviral Tip protein interactions with Lck, not primarily about CD28. While CD28 does bind Lck via the PYAP motif, the annotation appears to be derived from a study focused on a viral protein. Cannot fully assess the relevance of this annotation to CD28 without seeing the specific CD28 data in the paper. Supporting Evidence: PMID:15554700 Herpesvirus saimiri encodes a tyrosine kinase interacting protein (Tip) that binds to T-cell-specific tyrosine kinase Lck
GO:0005515 protein binding	IPI PMID:11285224 Mechanism for down-regulation of CD28 by Nef.	UNDECIDED	Summary: Publication not available for review. With/from indicates P03406 (a viral protein). This may relate to viral protein interactions with CD28. Reason: Publication not available. The with/from column indicates a viral protein (P03406). Cannot assess the annotation without the publication.
GO:0032743 positive regulation of interleukin-2 production	IDA PMID:3875683 Involvement of T44 molecules in an antigen-independent pathw...	ACCEPT	Summary: Early publication (1985) demonstrating CD28 involvement in IL-2 production. CD28 costimulation is one of the best-characterized drivers of IL-2 production in T cells. IL-2 is the canonical cytokine whose production is enhanced by CD28 signaling. Publication not available. Reason: Positive regulation of IL-2 production is a core downstream effect of CD28 costimulation. IL-2 is the signature cytokine induced by CD28 costimulation - this is the classical readout of CD28 function. The deep research review confirms CD28 promotes IL-2 production. Supporting Evidence: file:human/CD28/CD28-deep-research-falcon.md increases proliferation and expression of various cytokines in particular IL2 production in both CD4(+) and CD8(+) T-cell subsets PMID:1650475 B-cell surface antigen B7 provides a costimulatory signal that induces T cells to proliferate and secrete interleukin 2
GO:0042102 positive regulation of T cell proliferation	IDA PMID:3159820 Human T cell activation. II. A new activation pathway used b...	ACCEPT	Summary: Early publication (1988) demonstrating CD28 involvement in T cell proliferation. One of the foundational studies establishing CD28 as a costimulatory molecule. Publication not available. Reason: Positive regulation of T cell proliferation is a core function of CD28. This is one of the earliest demonstrations. Consistent with extensive subsequent literature.
GO:0042802 identical protein binding	NAS PMID:3159820 Human T cell activation. II. A new activation pathway used b...	ACCEPT	Summary: NAS annotation for identical protein binding, reflecting CD28 homodimerization. CD28 exists as a disulfide-linked homodimer on the cell surface. The 2022 NMR structure (PMID:35397202) characterized the dimerization interface in the transmembrane domain. Reason: CD28 homodimerization is well established. It exists as a disulfide-linked homodimer, and the transmembrane domain contains dimerization motifs (GxxxA). While identical protein binding is somewhat generic, it accurately describes CD28 homodimerization. Supporting Evidence: file:human/CD28/CD28-uniprot.txt Homodimer; disulfide-linked file:human/CD28/CD28-deep-research-falcon.md CD28 is a ~44 kDa disulfide-linked Ig-domain homodimer
GO:0045840 positive regulation of mitotic nuclear division	IDA PMID:3159820 Human T cell activation. II. A new activation pathway used b...	MARK AS OVER ANNOTATED	Summary: IDA annotation for positive regulation of mitotic nuclear division from the same 1988 publication. CD28 costimulation drives T cell proliferation which involves mitotic division. Reason: While CD28 costimulation does drive T cell proliferation (which involves mitosis), annotating CD28 specifically to positive regulation of mitotic nuclear division is an over-annotation. CD28 is a signaling receptor, not a direct regulator of the mitotic machinery. The proliferative effect is a downstream consequence of transcriptional and metabolic reprogramming, not a direct regulation of mitosis. The more appropriate annotation is positive regulation of T cell proliferation.
GO:0005515 protein binding	IPI PMID:9784967 CD28/B7 costimulation: a review.	MODIFY	Summary: IPI for protein binding with CD80 (P33681). Publication not available. Likely a review or primary study documenting CD28-CD80 interaction. Reason: Protein binding is uninformative for the CD28-CD80 core receptor-ligand interaction. Should be captured under coreceptor activity. Proposed replacements: coreceptor activity
GO:0005515 protein binding	IPI PMID:9784967 CD28/B7 costimulation: a review.	MODIFY	Summary: IPI for protein binding with CD86 (P42081). Same publication as above. Reason: Protein binding is uninformative for CD28-CD86 core receptor-ligand interaction. Should be captured under coreceptor activity. Proposed replacements: coreceptor activity
GO:0001819 positive regulation of cytokine production	TAS PMID:8717514 CD28/B7 system of T cell costimulation.	ACCEPT	Summary: TAS annotation for positive regulation of cytokine production. CD28 costimulation promotes production of multiple cytokines including IL-2, IL-4, IL-10, and others. Publication not available. Reason: Positive regulation of cytokine production is a well-established consequence of CD28 costimulation. While this is a somewhat broad term, CD28 does promote production of multiple cytokines (IL-2, IL-4, IL-10, IFN-gamma) making this parent term appropriate. Supporting Evidence: file:human/CD28/CD28-deep-research-falcon.md increases proliferation and expression of various cytokines in particular IL2 production PMID:8617933 IL-4 synthesis was greatly enhanced by triggering of CD40L on the T cell surface in conjunction with ligation of CD3/TCR and CD28
GO:0005886 plasma membrane	TAS PMID:9784967 CD28/B7 costimulation: a review.	ACCEPT	Summary: TAS annotation for plasma membrane from a review. Correct and consistent with all other evidence. Reason: Correct. CD28 is a plasma membrane protein.
GO:0006959 humoral immune response	TAS PMID:8717514 CD28/B7 system of T cell costimulation.	KEEP AS NON CORE	Summary: TAS annotation for humoral immune response. CD28 costimulation on T cells promotes T helper function that supports B cell antibody responses. Publication not available. Reason: While CD28 costimulation of T helper cells supports humoral immune responses (by promoting T cell help for B cells), this is a distal, pleiotropic consequence of CD28 function rather than a core molecular function. CD28 does not directly participate in antibody production or B cell processes.
GO:0007166 cell surface receptor signaling pathway	TAS PMID:9784967 CD28/B7 costimulation: a review.	ACCEPT	Summary: TAS annotation for cell surface receptor signaling pathway. CD28 is a cell surface receptor that signals upon ligand engagement. This is a broad parent term. Reason: Correct but broad. CD28 is a cell surface receptor and its engagement initiates signaling cascades. More specific terms (T cell costimulation, positive regulation of TCR signaling) provide better detail.
GO:0015026 coreceptor activity	TAS PMID:9784967 CD28/B7 costimulation: a review.	ACCEPT	Summary: TAS annotation for coreceptor activity. CD28 is the prototypic T cell coreceptor that cooperates with the TCR to enable full T cell activation. The GO definition of coreceptor activity fits CD28 precisely: combining with a messenger and in cooperation with a nearby primary receptor, initiating a change in cell activity. Reason: Coreceptor activity is the most precise molecular function term for CD28. CD28 acts in cooperation with the TCR (the primary receptor) by binding B7 ligands (the extracellular messengers) to initiate costimulatory signaling. This is the single best MF term for CD28. Supporting Evidence: file:human/CD28/CD28-deep-research-falcon.md CD28 is the prototypic co-stimulatory receptor (signal 2) that integrates with TCR signalling (signal 1) to enable full T cell activation
GO:0042102 positive regulation of T cell proliferation	TAS PMID:9784967 CD28/B7 costimulation: a review.	ACCEPT	Summary: TAS annotation for positive regulation of T cell proliferation from a review. Consistent with IDA and IBA annotations for the same term. Reason: Correct TAS annotation consistent with experimental evidence (IDA, IBA) for the same core function.
GO:0045070 positive regulation of viral genome replication	NAS PMID:7492435 Costimulation of CD4+ T cells via CD28 modulates human immun...	KEEP AS NON CORE	Summary: NAS annotation for positive regulation of viral genome replication. This likely relates to CD28 costimulation enhancing HIV replication in T cells, as activated T cells provide a more permissive environment for viral replication. Publication not available. Reason: CD28 does not directly regulate viral genome replication. Rather, CD28-mediated T cell activation creates an environment permissive for viral replication (e.g., HIV in activated T cells). This is a highly indirect downstream consequence of T cell activation, not a core function of CD28.
GO:0045727 positive regulation of translation	NAS PMID:12028592 The regulation of protein synthesis and translation factors ...	KEEP AS NON CORE	Summary: NAS annotation for positive regulation of translation. CD28 signaling is known to activate mTOR-dependent translation programs. Publication not available. Reason: While CD28 signaling does promote mTOR-dependent translation (particularly of IL-2 and other cytokine mRNAs), this is a downstream signaling consequence rather than a core function. CD28 is a receptor, not a translation regulator. Supporting Evidence: file:human/CD28/CD28-deep-research-falcon.md CD28 signalling promotes glycolytic flux and mTOR-dependent translation

Gene Description

Existing Annotations Review

Core Functions

CD28 is the prototypic T cell coreceptor. It cooperates with the TCR by binding B7 ligands (CD80/CD86) on APCs to provide signal 2 for T cell activation. This is the single most precise molecular function term for CD28.

References

Deep Research

Falcon

📚 Additional Documentation

Notes

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